Tag: QUAL

sam file error

sam file error 1 Hi, I was converting my sam file (after alignment with bowtie2) in bam format. I encountered the error: [E::sam_parse1] invalid QUAL character [W::sam_read1_sam] Parse error at line 11129453 command: samtools view -S -b -o input.bam ../alignment/input.sam Alignment works fine. This is the output: 22504890 reads; of…

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ftbfs and autopkgtest regression with htslib 1.19

Source: cyvcf2 Version: 0.30.22-1 Severity: important Tags: ftbfs upstream With the introduction of htslib 1.19 in experimental, cyvcf2 is experiencing test failures at package build time and autopkgtest time. The relevant part of the error looks like: cyvcf2/tests/test_reader.py …………………Fatal Python error: Aborted Current thread 0x00007fa7874de040 (most recent call first): File “/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cyvcf2/build/cyvcf2/tests/test_reader.py”, line 285…

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Tree size diversity is the major driver of aboveground carbon storage in dryland agroforestry parklands

Albrecht, A. & Kandji, S. T. Carbon sequestration in tropical agroforestry systems. Agric. Ecosyst. Environ. 1–3, 15–27 (2003). Article  Google Scholar  Nair, P. K. R. Agroforestry systems and environmental quality: Introduction. J. Environ. Qual. 40, 784–790 (2011). Article  CAS  PubMed  Google Scholar  Schroth, G. & McNeely, J. A. Biodiversity conservation,…

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LOINC 17546-3 Bartonella quintana rRNA [Presence] in Specimen by Probe

de-DE German (Germany) Bartonella quintana rRNA:Nachweis oder Schwellenwert:Zeitpunkt:XXX:Ordinal:Sonde es-AR Spanish (Argentina) ADN de Bartonella quintana:concentración arbitraria:punto en el tiempo:XXX:ordinal:sonda es-ES Spanish (Spain) Bartonella quintana rRNA:PrThr:Punto temporal:XXX:Ord:Sonda de DNA es-MX Spanish (Mexico) ARNr de Bartonella quintana:Presencia o umbral:Punto temporal:XXX:Ordinal:Investigacion fr-CA French (Canada) Bartonella quintana , ARNr:Présence-Seuil:Temps ponctuel:XXX:Ordinal:Sonde fr-FR French (France) Bartonella…

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Building reference dbSNP file using WGS samples

Building reference dbSNP file using WGS samples 2 Dear scientific community, I have to call variants from WGS samples of citrus. I used GATK pipeline for post processing of aligned reads but reference dbSNP file is not available for citrus sinensis. I am using bootstraping method. Removed duplicates and called…

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BBtools bug in reporting the number of substitutions in the console output, it seems to report insanely high rates of heterozygosity

Hello, I know Brian is sometimes around, but here is my command: while read p; do callvariants.sh in=${p}.recal.bam ploidy=2 vcf=${p}.20score.vcf useidentity=f overwrite=true ref=ref.fsa -Xmx50g ; done <ID java -ea -Xmx50g -Xms50g -cp /home/alessandro/software/bbmap/current/ var2.CallVariants in=ancestor.recal.bam ploidy=2 vcf=ancestor.20score.vcf useidentity=f overwrite=true ref=ref.fsa -Xmx50g Executing var2.CallVariants [in=ancestor.recal.bam, ploidy=2, vcf=ancestor.20score.vcf, useiden tity=f, overwrite=true, ref=Adineta_vaga.fsa,…

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SNPs of a specific mouse strain

Hi, I wonder how can I get SNPs for a particular mouse strain like C57BL6. I have downloaded a mouse reference vcf from ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.rsID.vcf.gz Its header is #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 129P2_OlaHsd 129S1_SvImJ 129S5SvEvBrd A_J AKR_J B10.RIII BALB_cByJ BALB_cJ BTBR_T+_Itpr3tf_J BUB_BnC3H_HeH C3H_HeJ C57BL_10J C57BL_10SnJ C57BL_6NJ…

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Issue with Merging BCF Files: Invalid INFO id Error

Issue with Merging BCF Files: Invalid INFO id Error 0 I am attempting to combine two BCF (Binary Variant Call Format) files into a single file using the command bcftools merge output1.bcf output2.bcf –force-samples -o test.bcf. However, when I try to view the resulting BCF file, I encounter an error…

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Clonal Hematopoiesis and Cardiovascular Disease in Patients With Multiple Myeloma Undergoing Hematopoietic Cell Transplant | Cardiology | JAMA Cardiology

Key Points Question  Is clonal hematopoiesis of indeterminate potential (CHIP) detected at the time of hematopoietic stem transplant (HCT) associated with increased rates of cardiovascular disease (CVD) among patients with multiple myeloma (MM) following HCT? Finding  In this cohort study of patients with MM undergoing HCT, CHIP was highly prevalent…

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Need Help Understanding Variant Calling Issues in De Novo Yeast Assembly

Need Help Understanding Variant Calling Issues in De Novo Yeast Assembly 0 We have two groups sample of yeast species, control (1 sample) and treatment (1 sample), whose complete reference genome isn’t available yet to do alignment nor variant calling. The objective of this project is straightforward, simply wanting to…

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The correlation between gut microbiome and atrial fibrillation: pathophysiology and therapeutic perspectives | Military Medical Research

Kim JE, Li B, Fei L, Horne R, Lee D, Loe AK, et al. Gut microbiota promotes stem cell differentiation through macrophage and mesenchymal niches in early postnatal development. Immunity. 2022;55(12):2300-17.e6. Article  CAS  PubMed  Google Scholar  Xiao W, Su J, Gao X, Yang H, Weng R, Ni W, et al….

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vcf – VEP annotation INFO field Ensembl IDs and locations

I have a vcf file that I annoteted with VEP, for human data. I have run VEP to annotate my files with some additional parameters (as shown below in the ##VEP-command-line). However, my output is rather strange (mainly the INFO column). ##VEP=”v108″ time=”2023-04-27 15:13:08″ cache=”workflow/resources/variants/cache_vep/homo_sapiens/108_GRCh38″ ensembl-funcgen=108.56bb136 ensembl-variation=108.a885ada ensembl-io=108.58d13c1 ensembl=108.d8a9c80 1000genomes=”phase3″…

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No valid entries in –score file

PLINK Error: No valid entries in –score file 0 Hi, I ran this command on plink1.9 to calculate the poligenic score. plink –vcf sample –score output.txt 1 2 3 –out poligenic_results – output.txt: ID ALT UKB-b-15541 rs10399793 C 0.000345793 rs2462492 T -0.00027716 – sample.vcf: #CHROM POS ID REF ALT QUAL…

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Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data

Study design Experiments were performed in accordance with the New Zealand Animal Welfare Act (1999) and institutional guidelines provided by the University of Auckland Animal Ethics Committee, which reviewed and approved these experiments under application R1003. We did not use any specific randomisation process to allocate animals to a particular…

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No samples in .vcf file.

I am trying to convert my vcf file into a BED format file.  When I use this command: plink –vcf merge.bacteria.vcf.gz –make-bed –out merge.bacteria.vcf.bed  I get the following error stating:  PLINK v1.90b6.21 64-bit (19 Oct 2020)          www.cog-genomics.org/plink/1.9/(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License…

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NGS one-liner to call variants

Tutorial:NGS one-liner to call variants 0 This is a tutorial about creating a pipeline for sequence analysis in a single line. It is made for capture/amplicon short read sequencing in mind for human DNA and tested with reference exome sequencing data described here. I share the process and debuging steps…

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NGS oneliner

Tutorial:NGS oneliner 0 This is a tutorial about creating a pipeline for sequence analysis in a single line.I share the process and debuging steps gone through while putting it together.Source is available at: github.com/barslmn/ngsoneliner/I couldn’t make a longer post, complete version of this post: omics.sbs/blog/NGSoneliner/NGSoneliner.html Pipeline # fastp –in1 “$R1″…

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Lack of correspondance of GFA node IDs to giraffe/call node IDs

I have a GFA graph built with PGGB using several samples. I want to genotype some other samples with short reads using VG Giraffe. After investigating how to generate the corresponding indexes for VG Giraffe from a GFA generated with PGGB, I think I have found a way to do…

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Generating Positional List from VCF

I think one of the ways to achieve your goal is by converting your VCF file to a MAF (Mutation Annotation Format) file. To this end, you may want to check out the fuc package I wrote: >>> from fuc import pyvcf, pymaf >>> data = { … ‘CHROM’: [‘chr1’,…

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Aligner with statistics included?

Aligner with statistics included? 1 Hello, Is there a long range aligner that could make a statistics outlook listing how many SNP, indels etc are observed in the alignment itself? Thank you aligner alignment • 203 views BBTools’ callvariants.sh calls variants only from the alignments. So: callvariants.sh in=nxyxx.bam ref=ref.fa yields:…

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Most sensible way to find private SNPs from a multisamples vcf with bcftools

Hello, this question is somehow complementary to what I asked yesterday here: Using bcftools to find unique alt homozygous sites Now let’s say I want to find the SNPs 0/1 unique to the sample D3A350g_bcftools2 (see below) I know I can use bcftools view -s D3A350g_bcftools2.bcf -x all_bcftools2_merged.vcf But there…

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How to interpret the Variant Allele Frequency??

How to interpret the Variant Allele Frequency?? 0 I am new to the field of Bioinformatics and seeking guidance. I am currently in the process of calculating the Variant Allele Frequency (VAF) using the VarScan software. I have obtained the results and have included screenshots for reference. I would greatly…

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public databases – Converting VCF format to text for use with PLINK and understanding column mapping

I successfully completed Nature PRS tutorial, which is based on PLINK. Turning to my real data, I downloaded ukb-d-20544_1.vcf.gz. Now I’m facing the problem that I seem to be unable to use it in PLINK or find the correct data format to download at all, and I am a bit…

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Using bcftools to find unique alt homozygous sites

Hello, I have a vcf with 20 samples. I want to find for each sample the sites that are 1/1, only in that sample (so other samples must have genotypes 0/1 or 0/0). I know I can use filters such as GT=”aa”‘ However, how do I say GT=”aa” for sample…

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Filter vcf SNPs by sample GT value

Filter vcf SNPs by sample GT value 1 I have a merged VCF file with multiple samples on joined SNP set, where original genotypes have a 0|0 / 0|1 / 1|0 / 1|1 genotype (GT) and merged are fomatted as 0/0 if SNP was missing (–missing-ref option of bcftools merge)….

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Imputation server failing to see samples in VCF files

Imputation server failing to see samples in VCF files 0 I used the following command to generate VCF files from the 23andMe zip file for the Michigan Imputation server but it keeps failing with the validation error: At least 20 samples must be uploaded. java -jar vcf-tools-0.1.jar vcf-generator –in 23_n_me/23andme-tools-output/genome_name_v4_Full_20230822212500.zip…

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Where to find info on VCF file format?

Where to find info on VCF file format? 1 The format of my vcf file is: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT chr8 1023470 chr8_1023470_T_G T G 48 . AF=3e-06;AQ=48 GT:DP:AD:GQ:PL:RNC What do AQ, AD and RNC mean? I tried looking here: samtools.github.io/hts-specs/VCFv4.1.pdf but couldn’t find them….

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Tomato growth stage modulates bacterial communities across different soil aggregate sizes and disease levels

Bhaduri D, Pal S, Purakayastha TJ, Chakraborty K, Yadav RS, Akhtar MS. Soil quality and plant-microbe interactions in the rhizosphere. In: Lichtfouse E, editor. Sustainable agriculture reviews: volume 17. Cham: Springer International Publishing; 2015. p. 307–35. Mishra S, Singh A, Keswani C, Saxena A, Sarma BK, Singh HB. Harnessing plant-microbe…

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filtering variants in a Strelka2 VCF file based on AD and AF

Dear all, I would appreciate having your suggestions on the following. I am working with a VCF file that was produced by Strelka on Tumor-Normal pairs. As it is well known, Strelka2 does not provide Allele Depth (AD) or VAF (variant allele fraction) in the VCF fields. I have used…

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VCF QUAL field for multiple samples

VCF QUAL field for multiple samples 1 Originally, I thought each line of a VCF file represented a single read that resulted in the detection of a variant. In that case, the QUAL field was straight forward, it was the quality of that read. However, when you have multiple samples,…

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manhattan plot with vcf information

manhattan plot with vcf information 0 Hello. I imported the VCF file and combined FIX and INFO to create a data frame. This data frame contains VCF file information such as CHROM, POS, REF, ALT, QUAL, FILTER, etc. I want to draw a manhattan plot with this data frame. The…

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Question about REDItools

Hi, I wanted to use REDItools to identify RNA editing events in my data. I had both RNA-seq and exome-seq data derived from the same sample. I download the latest version of REDItools (REDItools-1.2.1.zip, sourceforge.net/projects/reditools/files/) and test data (srv00.recas.ba.infn.it/reditools/data/testREDItools.tar.gz). When I run the scripts “REDItoolDnaRna.py” as “REDItoolDnaRna.py -i rna.bam -j…

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‘syscall’ is deprecated during installing jellyfish kmer counting

‘syscall’ is deprecated during installing jellyfish kmer counting 0 I have zero knowledge in bioinformatics. I’m using MacOS monterey and bash terminal for bioinformatics. Trying to install jellyfish to count kmer prior to DNA assembly. I’m using www.cs.cmu.edu/~ckingsf/software/jellyfish/README to help me install the tool. Can only do ./configure and already…

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How to install bbmap on Ubuntu 20.04 (Focal Fossa)?

Quick installation of bbmap Architecture: all Version: 38.79+dfsg-1: Step 1: Update system: sudo apt-get update Step 2: Install: bbmap Architecture: all Version: 38.79+dfsg-1 Ater updaing the OS run following command to install the packae: sudo apt-get install bbmap Architecture: all Version: 38.79+dfsg-1 Package Details Package: bbmap Architecture: all Version: 38.79+dfsg-1 Version: 38.79+dfsg-1 Maintainer: Ubuntu Developers Home page: sourceforge.net/projects/bbmap/…

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GATK AnnotateVcfWithBamDepth returns zero DP for all variants in VCF

Dear all, I am using GATK (v4.1.9.0) AnnotateVcfWithBamDepth to get the DP for all variants in ClinVar VCF in a retina RNA-seq BAM file. However, the tool returns zero depth for all variants in the VCF, even though I checked multiple variants in IGV and I saw that they are…

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Converting custom VCF to standard VCF

Hello! I have received some custom vcfs (yes, I know, and I hate it) containing information of each sample per row, independent of variant. This means that some variants are repeated. I have the following columns: columns 1-17 #CHROM POS GENE REF ALT QUAL FILTER INFO PTID AF AQ GT…

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vcf file chr notation

“I have a single VCF file named ‘ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz’. The issue at hand is that the file uses different chromosomal notation and lacks the ‘chr’ prefix. Like this “##fileformat=VCFv4.3 ##FILTER=<ID=PASS,Description=”All filters passed”> ##fileDate=11032019_15h52m43s ##source=IGSRpipeline ##reference=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa ##contig=<ID=1> ##contig=<ID=2> ##contig=<ID=3> ##contig=<ID=4> ##contig=<ID=5> ##contig=<ID=6> ##contig=<ID=7> ##contig=<ID=8> ##contig=<ID=9> ##contig=<ID=10> ##contig=<ID=11> ##contig=<ID=12> ##contig=<ID=13> ##contig=<ID=14> ##contig=<ID=15> ##contig=<ID=16>…

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Liftedover vcf header/contig compatibility

I have a collaborator that has lifted over their hg19 files to hg38 using Crossmap. The first step in the workflow they need to run is a simple bcftools filter for variant quality. They are getting an unknown file type error. Are there any obvious problems with this header that…

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Expanding gVCF box from GATK

Expanding gVCF box from GATK 0 Hello, I wanted to expand the gVCF block of my vcf but I got this as a result ##bcftools_convertCommand=convert –gvcf2vcf -f Adineta_vaga.fsa; Date=Tue Aug 1 11:51:21 2023 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ancestor Chrom_3 793 . G T 172.33 ….

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bcftools view to failed reader data

It’s so confused for data editing with vcftools – bcftools fusion preprocessing. I want to view all results in bcftools, vcftool and zcat when I typing command, but it doesn’t work. for example, i want to see same results with bcftools view input.file | less [environment]$ bcftools view input.vcf.gz |…

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LOINC 23530-9 Trypanosoma evansi rRNA [Presence] in Specimen by Probe

es-AR Spanish (Argentina) ADN de Trypanosoma evansi:concentración arbitraria:punto en el tiempo:XXX:ordinal:sonda es-ES Spanish (Spain) Trypanosoma evansi rRNA:PrThr:Punto temporal:XXX:Ord:Sonda de DNA es-MX Spanish (Mexico) ARNr de Trypanosoma evansi:Presencia o umbral:Punto temporal:XXX:Ordinal:Investigacion fr-CA French (Canada) Trypanosoma evansi , ARNr:Présence-Seuil:Temps ponctuel:XXX:Ordinal:Sonde fr-FR French (France) Trypanosoma evansi ARNr:Présence/Seuil:Ponctuel:Milieux divers:Qualitatif:PCR fr-BE French (Belgium) Trypanosoma evansi…

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LOINC 29596-4 CD25 Ag [Presence] in Tissue by Immune stain

es-AR Spanish (Argentina) CD25:concentración arbitraria:punto en el tiempo:tejido, no especificado:ordinal:tinción inmunológica es-ES Spanish (Spain) CD25 Antígeno:PrThr:Punto temporal:Tejido:Ord:Tinción de inmunohistoquímica es-MX Spanish (Mexico) CD25 Ag:Presencia o umbral:Punto temporal:Tejido y frotis:Ordinal:Mancha inmune et-EE Estonian (Estonia) CD25 antigeen:PrThr:Pt:Tis:Ord:ImmuunvärvSynonyms: Järgarvuline Juhuslik Kude fr-CA French (Canada) CD25 , Ag:Présence-Seuil:Temps ponctuel:Tissu:Ordinal:Coloration immunologique fr-FR French (France) CD25…

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Clarification for bcftools consensus

Clarification for bcftools consensus 1 Hi all, I have a .vcf file I generated using bcftools mpileup and then filtered to retain positions of interest. I now want to generate a consensus sequence using bcftools consensus. The issue I’ve had so far is that positions in the .vcf file that…

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Plotting Genomic Overlaps with GRanges

I have come up with two approaches using two different findOverlaps methods (Genomic Alignments R package) for which I have opted to use subsetbyOverlaps as this suits my needs better. I’m trying to plot the genomic coordinates that overlap, was trying with the GViz package but not sure if this…

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problem

this is my vcf file i don’t understand MAXGT and POLY. how to remove MAXGT AND POLY, i am go to gwas study but thia MAXGT AND POLY was my problem . pls any one help me. ##fileformat=VCFv4.1 ##fileDate=20130319 ##source=GenerateReportDataAndVCFv2.2.2.0 ##reference=HumanNCBI37_UCSC ##phasing=none ##INFO=<ID=DP,Number=1,Type=Integer,Description=”Total Depth”> ##INFO=<ID=TI,Number=.,Type=String,Description=”Transcript ID”> ##INFO=<ID=GI,Number=.,Type=String,Description=”Gene ID”> ##INFO=<ID=EXON,Number=0,Type=Flag,Description=”Exon Region”>…

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Systems biology approaches to identify potential targets and inhibitors of the intestinal microbiota to treat depression

Dean, J. & Keshavan, M. The neurobiology of depression: An integrated view. Asian J. Psychiatry 27, 101–111 (2017). Article  Google Scholar  Ng, M. et al. Global, regional, and national prevalence of overweight and obesity in children and adults during 1980–2013: A systematic analysis for the Global Burden of Disease Study…

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131releng-armv7-quarterly][biology/htslib] Failed for htslib-1.17 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: j…@freebsd.org Log URL: pkg-status.freebsd.org/ampere1/data/131releng-armv7-quarterly/bee14067723b/logs/htslib-1.17.log Build URL: pkg-status.freebsd.org/ampere1/build.html?mastername=131releng-armv7-quarterly&build=bee14067723b Log: =>> Building biology/htslib build started at Mon Jul 10…

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FASTQ Phred33 average base quality score

FASTQ Phred33 average base quality score 2 I have a FASTQ dataset where I’m trying to find the average base quality score. I found this old link that helped somewhat (www.biostars.org/p/47751/). Here is my script (I’m trying to stick to awk, bioawk or python): bioawk -c fastx ‘{print “>”$name; print…

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FORMAT column with GT for somatic SV VCFs

FORMAT column with GT for somatic SV VCFs 0 Hi, I have done tumor-only somatic structural variant (SV) calling with Manta. This results in several VCFs with candidate variants. However, some of these do not contain GT in FORMAT (GitHub issue). In tumor-only mode I do not get somaticSV.vcf.gz as…

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what is a medication mishap

what is a medication mishap When the number of prescriptions rises, it is more common to confuse the medications. Webnoun [ C or U ] uk / ms.hp / us / ms.hp / Add to word list C2 bad luck, or an unlucky event or accident: The parade was very…

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Very different QUAL scores on VCFs of same sample using different methods

Hello, I produced a few VCFs, using clara parabricks deepvariant and gatk haplotype caller (in the regular way and also using clara-parabricks haplotype caller, which yielded identical results) The problem is that the QUAL score of both different extremely; using haplotype caller a lot of variants were in the thousands,…

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VCF record format error when trying to run Beagle 5.4

Hi everyone, I am trying to run the Beagle 5.4 software where it needs to read a VCF file. The error message I have is: Exception in thread “main” java.lang.IllegalArgumentException: VCF record format error: 1 131079320 BHD0100437271 G A . PASS . GT at vcf.VcfRecGTParser.ninthTabPos(VcfRecGTParser.java:87) at vcf.VcfHeader.isDiploid(VcfHeader.java:73) at vcf.RefIt.<init>(RefIt.java:130) at…

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The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes

Purohit, J., Kumar, A., Hynniewta, M. & Satyawada, R. R. Karyomorphological studies in guar (Cyamopsis tetragonoloba (Linn.) Taub.)—An important gum yielding plant of Rajasthan, India. Cytologia 76(2), 163–169 (2011). Article  Google Scholar  Gillett, J. B. Indigofera (Microcharis) in tropical Africa with the related genera Cyamopsis and Rhynchotropis. H.M.S.O Kew Bull.,…

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GenomicsDBImport from Mutect2 output

I am trying to follow GATK 4.2.0 best-practice guidelines for Mutect2 PoN creation. I called variants in my samples as recommended with: gatk Mutect2 \ -R ${REF} \ -L ${EXOME_INPUT_INTERVALS} \ -I ${BAM} \ –sequence-dictionary ${DICT} \ –max-mnp-distance 0 \ -O ${SAMPLE_NAME}.mutect2.vcf but I see that the tool is unable…

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object of type ‘NoneType’ has no len()

I run Truvari for benchmarking of 2 vcf files truvari bench -b NA12878_S1.genome.vcf.gz -c b1.vcf.gz -o out. However, it gives the following error. First vcf file contains format, info, filter, contig and maxdepth headers, which is the vcf file I found on Internet. The second vcf file is output of…

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How to extract read counts at the mutation locations

I have a scDNAseq dataset having multiple FASTQ files for multiple single cells. samtools was used after aligning FASTQ files with BWA to hg19 reference to produce bam files. I have already identified 36 SNV mutation sites and I want to use mpileup to extract read counts (Total read count…

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Retrieving Therapy information from CiViC VCF files

Retrieving Therapy information from CiViC VCF files 1 Hi all! I downloaded CiViC’s Accepted & Submitted Variants VCF from civicdb.org/releases/main. The INFO column format for the variants look like this: ##INFO=<ID=CSQ,Number=.,Type=String,Description=”Consequence annotations from CIViC. Format: Allele|Consequence|SYMBOL|Entrez Gene ID|Feature_type|Feature|HGVSc|HGVSp |CIViC Variant Name|CIViC Variant ID|CIViC Variant Aliases|CIViC Variant URL|CIViC Molecular Profile Name|CIViC…

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LOINC 6421-2 Hepatitis B virus rRNA [Presence] in Specimen by Probe

de-DE German (Germany) Hepatitis-B-Virus rRNA:Nachweis oder Schwellenwert:Zeitpunkt:XXX:Ordinal:SondeSynonyms: HBV es-AR Spanish (Argentina) ARNr del virus de la hepatitis B:concentración arbitraria:punto en el tiempo:XXX:ordinal:sonda es-ES Spanish (Spain) Virus Hepatitis B rRNA:PrThr:Punto temporal:XXX:Ord:Sonda de DNA es-MX Spanish (Mexico) ARNr del virus de la hepatitis B:Presencia o umbral:Punto temporal:XXX:Ordinal:Investigacion fr-CA French (Canada) Virus de…

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LOINC 79211-9 Fetal Chromosome X and Y aneuploidy risk [interpretation] in Plasma cell-free DNA Qualitative by Sequencing

Term Description The risk interpretation (e.g. increased risk) of chromosome X & Y aneuploidy present in fetal cell-free DNA from maternal plasma. This term was created for, but not limited in use to, QNatal Advanced, a non-invasive prenatal test which uses massively parallel sequencing to identify chromosome X & Y…

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Processing WES VCF for case control GWAS analysis

Dear community I’m currently trying to try a GWAS for case control study using PLINK using whole exome VCF files. I understand that I need to convert these VCF files into PLINK’s binary format (bed/bim/fam) before I can proceed with the GWAS. From my literature I have to manually create…

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convert fasta to fastq without quality score input file

Here’s another beginner BioPython question from me… I’m running some genome assemblies for someone who has some new Illumina sequence data and also had done some sequencing a few years ago. They have some Sanger and 454 sequences (a couple thousand sequences with a couple thousand base pairs for each)…

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gatk Hardfilter Error

gatk Hardfilter Error 0 Hello, I run the code but I got the Error. Could you pls help me with this issue? How can I fix it? gatk VariantFiltration -R reference. fasta -V input.vcf –filter-expression “FILTER == ‘PASS’ && (QUAL < 30.0 || QD < 2.0 || FS > 60.0…

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Microsatellite markers reveal genetic diversity and population structure of Portunus trituberculatus in the Bohai Sea, China

Liu, L. et al. Identification of quantitative trait loci for growth-related traits in the swimming crab Portunus trituberculatus. Aquacult. Res. 46, 850–860 (2015). Article  CAS  Google Scholar  Sun, Q. F. et al. Astaxanthin: The ubiquitous and abundant carotenoid as a pivotal interior factor of anti-oxidation and immune for the moulting…

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problems with MAF for MutSigCV (vcf2maf)

I am trying to run MutSIgCV and got stuck with this error: MutSigCV allsamples.md.tc.ir.br.pr.ug.dbsnp.vep.maf \ “$anno”exome_full192.coverage.txt \ “$anno”gene.covariates.txt \ my_results \ “$anno”mutation_type_dictionary_file.txt \ “$anno”chr_files_hg19 ====================================== MutSigCV v1.4 (c) Mike Lawrence and Gaddy Getz Broad Institute of MIT and Harvard ====================================== MutSigCV: PREPROCESS ——————– Loading mutation_file… Error using MutSigCV>MutSig_preprocess (line 246)…

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DanMAC5: a browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals | BMC Genomic Data

Demographics Data from three studies were included: Dan-NICAD: 1,649 individuals with symptoms of obstructive coronary artery disease, predominantly chest pain, undergoing coronary computed tomography angiography. In total, 52% were females, the mean age was 57 years (+/- 9 SD), median coronary artery calcium score were 0 [0–82] and 24% of…

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A review on blockchain for DNA sequence: security issues, application in DNA classification, challenges and future trends

Abadi M, Agarwal A, Barham P, et al. 2016 TensorFlow: large-scale machine learning on heterogeneous distributedsystems. Cornell University Library website. arxiv.org/abs/1603.04467. Published 2016. Accessed October 2016. Afshar P, Mohammadi A, Plataniotis KN. (2018) Brain tumor type classification via capsule networks, in Proc. 25th IEEE Int Conf Image Process. pp. 3129–3133….

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The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae

Elston KM, Leonard SP, Geng P, Bialik SB, Robinson E, Barrick JE. Engineering insects from the endosymbiont out. Trends Microbiol. 2022;30:79–96. Article  CAS  PubMed  Google Scholar  Brophy JAN, Triassi AJ, Adams BL, Renberg RL, Stratis-Cullum DN, Grossman AD, et al. Engineered integrative and conjugative elements for efficient and inducible DNA…

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Splitting of VCF file of CSQ field in the INFO column to tabular format.

VCF file will be having seven fixed columns and INFO column. Chromosome, position, ID, ref, alt, qual, filter, and INFO column. This INFO column will be having the variant related information. In the INFO column CSQ field will be having multiple fields – 82 fields fixed with the delimeter “|”…

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how can I generate a VCF (in hg38 coords) of differences between hg38 and CHM13?

I downloaded s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph/hprc-v1.0-minigraph-grch38.gfa.gz which contains hg38, chm13, and other assemblies, and now am trying to use vg to generate a VCF with the variants in CHM13 relative to hg38. After converting to vg format, by running vg convert <(gunzip -c hprc-v1.0-minigraph-grch38.gfa.gz) > hprc-v1.0-minigraph-grch38.vg, I tried a few different variations of…

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PLINK: Whole genome data analysis toolset – dbSNP

1. Introduction 2. Basic information 3. Downloads and general notes 4. Command reference table 5. Basic usage/data formats 6. Data management 7. Summary stats 8. Inclusion trim 9. Population stratification 10. IBS/IBD estimation 11. Bond 12. Family-based community 13. Permutation process 14. LD calculations 15. Multimarker tests 16. Conditional haplotype…

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sequence analysis – How can I make this Biopython program (to correct erroneous barcodes) run faster, and is there any alternative method?

This question was migrated from Biology Stack Exchange because it can be answered on Bioinformatics Stack Exchange.Migrated yesterday. This question has also been asked on Biostars I am looking forward to getting a valuable suggestion for a bioinformatic problem. Background: Currently, I am performing a de novo whole…

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vcf.Reader() in Python doesn’t read my VCF

vcf.Reader() in Python doesn’t read my VCF 0 I was working on a building a GUI with wxPython and wanted to import a VCF file with open(file_path, ‘r’) as file: vcf_reader = vcf.Reader(file) for record in vcf_reader: # Access the fields of each VCF record as needed chrom = record.CHROM…

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Metagenome and metabolome insights into the energy compensation and exogenous toxin degradation of gut microbiota in high-altitude rhesus macaques (Macaca mulatta)

Ma, Y. et al. Gut microbiota adaptation to high altitude in indigenous animals. Biochem. Biophys. Res. Commun. 516, 120–126 (2019). Article  CAS  PubMed  Google Scholar  Guo, N. et al. Seasonal dynamics of diet-gut microbiota interaction in adaptation of yaks to life at high altitude. NPJ Biofilms Microbiomes 7, 38 (2021)….

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I want to correct the erroneous barcode file, and the Python code that I’ve written, using Biopython, is very slow. How can I make this process faster, and is there any alternative method?

I am looking forward to getting a valuable suggestion for a bioinformatic problem. Background: Currently, I am performing a de novo whole genome assembly. At the stage of barcode correction, I lost nearly half of all the reads due to erroneous barcodes. While library construction, 18-base molecular barcodes were used…

Continue Reading I want to correct the erroneous barcode file, and the Python code that I’ve written, using Biopython, is very slow. How can I make this process faster, and is there any alternative method?

Calculating Variant Allele Frequency

I got a VCF which I need to calculate variant allele frequency for each variant at each position. My understanding is that variant allele frequency is AD / DP There are multiple sample for each position (NA0001, NA0002, NA0003). Do I get the average for each of them as they…

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why CombineGCVFs in gatk not showing all the samples name?

why CombineGCVFs in gatk not showing all the samples name? 0 Hi, I combined the 64 .vcf files using the CombineGVCFs in gatk. The command was completed successfully but its showing the output with only one column and why not rest of the 64 samples? The output is here #CHROM…

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Invalid QUAL value on line

PLINK Error: Invalid QUAL value on line 0 Dear all, I have worked with VCF file after haplotypecaller, where QUAL=Infinity for some variants. I am trying to make PGEN format, but I have this ERROR: Error: Invalid QUAL value on line 17 of test_123-temporary.pvar.zst. The default range for QUAL is…

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How to add attributes (i.e. gene_id, transcipt_id, exon_id, etc.) annotation from .bed file onto VCF?

I’m trying to annotate genes onto a VCF file with bcftools. My annotation file is a .bed file that originally was a hg38 UCSC knownGene gtf file, converted by BEDOPS: hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/ Original GTF file: chr1 11868 12227 . . + knownGene exon . gene_id “ENST00000456328.2”; transcript_id “ENST00000456328.2”; exon_number “1”; exon_id…

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LOINC 5034-4 Streptococcus agalactiae rRNA [Presence] in Specimen by Probe

zh-CN Chinese (China) 无乳链球菌 rRNA:存在情况或阈值:时间点:XXX:序数型:DNA探针Synonyms: B 族链球菌 rRNA B 族链球菌;B 组链球菌;B 群链球菌;GBS B 组链球菌 rRNA B 群链球菌 rRNA 不明的;其他;将在相应消息内其他部分之中加以详细说明;未作详细说明的;未作说明的;未做说明的标本;未加规定的;未加说明的标本;杂项 依次型;分类顺序型;定性的;序数型(或称等级型);性质上的;有序型;有序性分类应答;有序性分类结果;秩次型;等级型;筛查;顺序型 存在情况;存在;存在与否;是否存在;阈值;界值;界限;阀值;临界值;存在情况(存在、存在与否、是否存在)或阈值(界值、界限、阀值、临界值) 微生物学;微生物学试验;微生物学试验(培养、DNA、抗原及抗体) 时刻;随机;随意;瞬间 核糖体核糖核酸;核糖核酸 RNA 核蛋白体 RNA 核蛋白体 RNA(Ribosomal RNA,RRNA) 核蛋白体核糖核酸 核醣体 RNA 脱氧核糖核酸探针 es-AR Spanish (Argentina) ARNr de Streptococcus agalactiae:concentración arbitraria:punto en el tiempo:XXX:ordinal:sonda fr-CA French (Canada) Streptococcus agalactiae…

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What is the major problem with this pipeline of SNPs analysis?

First, I have several Aspergillus flavus (A kind of fungi species) illumina sequencing raw data as pair of fastq.gz file (sample1_filtered_1.fastq.gz and sample1_filtered_2.fastq.gz). And I wanted to assemble illumina fragment sequences and make SNP(single nucleotide polymorphism) analysis with the reference genome, Aspergillus flavus NRRL3357 as fasta file. At the end…

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Problem to convert genotypes to plink format from bcftools

I had a vcf file with imputed genotypes from beagle like this: ##fileformat=VCFv4.2 ##filedate=20210504 ##source=”beagle.18May20.d20.jar” ##INFO=<ID=AF,Number=A,Type=Float,Description=”Estimated ALT Allele Frequencies”> ##INFO=<ID=DR2,Number=1,Type=Float,Description=”Dosage R-Squared: estimated squared correlation between estimated REF dose [P(RA) + 2*P(RR)] and true REF dose”> ##INFO=<ID=IMP,Number=0,Type=Flag,Description=”Imputed marker”> ##FORMAT=<ID=GT,Number=1,Type=String,Description=”Genotype”> ##FORMAT=<ID=DS,Number=A,Type=Float,Description=”estimated ALT dose [P(RA) + 2*P(AA)]”> ##FORMAT=<ID=GP,Number=G,Type=Float,Description=”Estimated Genotype Probability”> #CHROM POS ID…

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Example of overlapping vcf calls with *

I’m looking for help understanding the example of spanning alleles and multi-allelic loci on luntergroup.github.io/octopus/docs/guides/advanced/vcf/ The ALT field values are OK, but the GT values don’t make sense to me. BAM files in IGV-style display show 3 samples. 1st, HG002, has a 4-bp del starting at 728 in half the…

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plink2 export tped 12 not working as expected

Hi, When I take a VCF file, convert it to plink, and then export it as a tped, the modifier ’12’ does not work as expected. I thought this modifier causes ALT1 alleles to be coded as ‘1’ and REF alleles as ‘2’. However, it appears to code REF alleles…

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Variant caller reports a homozygous variant genotype, but more reads are associated with reference

Variant caller reports a homozygous variant genotype, but more reads are associated with reference 0 Hi there, I’m confused about how to interpret this output from calling variants using bcftools: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GSM5292852 1065632 chr9 41242177 . T C 6.65947 . DP=37;VDB=0.133454;SGB=-0.662043;RPBZ=2.91136;MQBZ=4.0715;BQBZ=1.05041;SCBZ=-0.480069;MQ0F=0;AC=2;AN=2;DP4=0,26,0,9;MQ=5 GT:PL:AD…

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Variant Calling with Multiple Individuals in Freebayes

Variant Calling with Multiple Individuals in Freebayes 1 Hello, I am currently a new student in Bioinformatics and was trying to do variant calling with Freebayes software. I have 10 individuals and also have a reference genome. I have already sorted and indexed all my .bam files ready for variant…

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mpileup2sync

mpileup2sync 0 Hello there, I’m new to doing this type of analysis. I’m trying to convert a mpileup file into the synchronized file format (sync) but I have a problem using the script that I found. This is the script: mpileup2sync –input pools_all.mpileup –output pools_all.sync –fastq-type sanger –min-qual 20 –threads…

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TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene

I am trying to annotate a list of SNPs using the hg38 genome (knownGene) and locateVariants(). The program is able to successfully run and provide “GeneIDs” for several of the loci. However, some GeneIDs are applied to SNPs in completely different regions and on completely different chromosomes. When I cross…

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Picking the Perfect Data Visualization: Barplots

Data Science How-To’s Python Tutorials This blogpost is the second in a series where we explain the most common data visualization types and how you can best use them to explore your data and tell its story. In this post, we’ll cover barplots, which can give us great insight into…

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LOINC 76575-0 Bacterial 16S rRNA [Presence] in Specimen by NAA with probe detection

Term Description This term was created for, but is not limited in use to, Pathogenius Laboratories’ Level 1 Wound and/or ENT test panels, which use quantitative PCR to identify commonly-found microorganisms in wound or ear, nose, and throat samples, respectively. Source: Regenstrief LOINC Part Description LP189395-9   Bacterial 16S rRNASequencing…

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Can not get bcftools norm to join biallelics into a multiallelic.

Forum:Can not get bcftools norm to join biallelics into a multiallelic. 0 is this the right way to use bcftools to join/merge biallelic records into a multiallelic? If so, it is not working. No errors but it gives me the same file with my command added to the headers. Example…

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LOINC 16584-5 Chlamydophila pneumoniae rRNA [Presence] in Sputum by Probe

zh-CN Chinese (China) 肺炎嗜性衣原体 rRNA:存在情况或阈值:时间点:痰液:序数型:DNA探针Synonyms: CPN;Twar 制剂;Twar 株;肺炎衣原体;肺炎衣原体 Twar 株;鹦鹉热衣原体TWAR-TW株 下呼吸道;痰 亲衣原体 亲衣原体属 依次型;分类顺序型;定性的;序数型(或称等级型);性质上的;有序型;有序性分类应答;有序性分类结果;秩次型;等级型;筛查;顺序型 嗜性衣原体属 嗜衣体 嗜衣体属 嗜衣原体 嗜衣原体属 存在情况;存在;存在与否;是否存在;阈值;界值;界限;阀值;临界值;存在情况(存在、存在与否、是否存在)或阈值(界值、界限、阀值、临界值) 微生物学;微生物学试验;微生物学试验(培养、DNA、抗原及抗体) 时刻;随机;随意;瞬间 核糖体核糖核酸;核糖核酸 RNA 核蛋白体 RNA 核蛋白体 RNA(Ribosomal RNA,RRNA) 核蛋白体核糖核酸 核醣体 RNA 脱氧核糖核酸探针 衣原体 衣原体属 fr-CA French (Canada) Chlamydophila pneumoniae , ARNr:Présence-Seuil:Temps ponctuel:Expectorations:Ordinal:Sonde es-AR Spanish (Argentina) ADN de Chlamydophila pneumoniae:concentración…

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Getting matrix of QDs from VCF file

Getting matrix of QDs from VCF file 1 Hi, I have a vcf file and I would like to get a site-by-individual matrix of read depths (the DP label) and a second matrix of just the GQ scores. What is the easiest way to do this? Thanks in advance! Ex…

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Genome-wide significant risk loci for mood disorders in the Old Order Amish founder population

GBD 2017 Disease and Injury Incidence and Prevalence Collaborators. Global, regional, and national incidence, prevalence, and years lived with disability for 354 diseases and injuries for 195 countries and territories, 1990-2017: a systematic analysis for the Global Burden of Disease Study 2017. Lancet. 2018;392:1789–858. Article  Google Scholar  Smoller JW, Finn…

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Filtering of tricky overlapping sites in VCF

I’m working on a project where I’m working with variants ranging from low frequency (AF~=0.03) up to high frequency (AF=1) after variant calling with lofreq. There are some cases where positions in the vcf are duplicated and this is leading to issues with my downstream processing of the data. Consider…

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Survival outcomes of patients newly diagnosed with diffuse large B-cell lymphoma: real-world evidence from a German claims database

Adzersen K, Friedrich S, Becker N (2016) Are epidemiological data on lymphoma incidence comparable? Results from an application of the coding recommendations of WHO, InterLymph, ENCR and SEER to a cancer registry dataset. J Cancer Res Clin Oncol 142:167–175 Article  PubMed  Google Scholar  Ardeshna KM, Smith P, Norton A et…

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Health-related quality of life with pembrolizumab or placebo plus chemotherapy with or without bevacizumab for persistent, recurrent, or metastatic cervical cancer (KEYNOTE-826): a randomised, double-blind, placebo-controlled, phase 3 trial

Summary Background In the KEYNOTE-826 study, the addition of the anti-PD-1 monoclonal antibody pembrolizumab to chemotherapy with or without bevacizumab improved overall survival and progression-free survival (primary endpoints) versus placebo plus chemotherapy with or without bevacizumab, with manageable toxicity, in patients with persistent, recurrent, or metastatic cervical cancer. In this…

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LOINC 5024-5 Mycobacterium gordonae rRNA [Presence] in Specimen by Probe

zh-CN Chinese (China) 戈登分枝杆菌 rRNA:存在情况或阈值:时间点:XXX:序数型:DNA探针Synonyms: AFB 不明的;其他;将在相应消息内其他部分之中加以详细说明;未作详细说明的;未作说明的;未做说明的标本;未加规定的;未加说明的标本;杂项 依次型;分类顺序型;定性的;序数型(或称等级型);性质上的;有序型;有序性分类应答;有序性分类结果;秩次型;等级型;筛查;顺序型 分支杆菌 分支杆菌属 分枝杆菌属 劳瘵 存在情况;存在;存在与否;是否存在;阈值;界值;界限;阀值;临界值;存在情况(存在、存在与否、是否存在)或阈值(界值、界限、阀值、临界值) 微生物学;微生物学试验;微生物学试验(培养、DNA、抗原及抗体) 戈氏分支杆菌 rRNA 戈氏分支杆菌;戈氏分枝杆菌;戈登分支杆菌 戈氏分枝杆菌 rRNA 戈登分支杆菌 rRNA 抗酸 抗酸杆菌 抗酸杆菌(Acid fast bacillus,AFB) 抗酸菌 时刻;随机;随意;瞬间 核糖体核糖核酸;核糖核酸 RNA 核蛋白体 RNA 核蛋白体 RNA(Ribosomal RNA,RRNA) 核蛋白体核糖核酸 核醣体 RNA 痨 痨病 结核 结核病 肺结核 脱氧核糖核酸探针 es-AR Spanish (Argentina) ARNr de Mycobacterium…

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problem with chromosomes in michigan imputation server

problem with chromosomes in michigan imputation server 4 Hi, I am trying to impute a dataset using the Michigan imputation server but I got this error: No valid chromosomes found! I have vcf (with tabix index) files from 1-23 chromosomes that look like this: Should I add chr at the…

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summary | Finding WGCNA modules that are “absent” from the healthy cells and so “exclusive” to cancer cells ?

Hello, I am currently using the hdWGCNA package on single cell data. So I get modules on a scRNAseq of cancer cells that I project on healthy cells in order to see what are the modules that are “absent” from the healthy cells and so “exclusive” to cancer cells. To…

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how to seperate VEP INFO column into seperate columns

I have a vcf files like below: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT treatmentSample chr1 857100 . C T 1756.06 PASS AC=2;AF=1;AN=2;DP=60;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=29.27;SOR=1.812;CSQ=chr1:857100|T|SNV|ENSG00000228794|ENST00000445118|LINC01128||1|MODIFIER|non_coding_transcript_exon_variant||||5/5|||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,60:60:99:1770,180,0 Does anyone know how to seperate INFO columns into different columns? And also how to separate treatmentSample column following the FORMAT ORDER? I…

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