Tag: mpileup

All radiocarbon dates were calibrated in OxCal 4.4 using the IntCal20 calibration curve18,19. There is no stable carbon and nitrogen isotopic evidence for any detectable input of marine or freshwater foods that would require a correction for reservoir effects. Charterhouse Warren: Archaeological context Charterhouse Warren is a natural shaft in…

1. Introduction Tuberculosis (TB) is a significant global burden and is widely reported to be a major public health and economic problem, costing the world $617 billion between 2000 and 2015 and projected to cost $1 trillion between 2015 and 2030 (1). It is the second leading cause of death…

Mutant collection development We mutagenized 2,700 seeds of the wheat–Th. elongatum introgression line RWG34 containing Sr43 (ref. 29). Dry seeds were incubated for 16 h with 200 ml of a 0.8% (w/v) EMS solution with constant shaking on a Roller Mixer (Model SRT1, Stuart Scientific) to ensure maximum homogenous exposure of the…

Plant material Bread wheat accessions Transfer (TA5524), WL711, TA5605, Ae. umbellulata accession TA1851 and Ae. triuncialis accession TA10438 were obtained from the Wheat Genetics Resource Center (WGRC). TcLr9 (Transfer/6*Thatcher) is a near-isogenic line carrying Lr9 from Transfer in the genetic background of the susceptible wheat line Thatcher. TcLr9 and TA5605…

I’m using bcftools to extract variants from a bam file, but I have reference data that tells me whether the patient is homozygous or heterozygous. For a particular sample, I see a high proportion of the alternate allele (87%) and a lower proportion of the reference allele (13%), yet according…

Detect mutations in clonally propagated plants 0 I am analysing Illumina whole-genome resequencing data from two clonally propagated plants aiming to find any potential variants that are unique to either of the two. Note that these would be expected to be somatic mutations and that due to the nature of…

Variant calling using samtools 1 Hi all, I modified my output as a vcf file but not bcf as the instruction. Is that OK or the output is not correct? Thank you so much! bcftools mpileup -f Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa finalBamFile2.bam | bcftools call -mv -Ob -o variants.vcf.gz bcftools mpileup -f reference.fa…

Nextflow process for samtools sort and variant calling 2 Hi everybody ! I’m currently try to learn nextflow scripting. I’m a novice and I just begin with a script in order to sort and convert a SAM file to a BAM file and then call variants thanks to a reference…

I am not using any variant caller Use a variant caller. bcftools, at least, will output variant frequency per variant: bcftools mpileup -ugf ref.fa sample.bam | bcftools call -mv > output.vcf As an alternative approach, I wrote some code to parse the mpileup output and extract counts for different alleles;…

mpileup read base output 0 I am running mpileup and generally understand the output of the column containing the bases found at a certain position. However, this is added onto the end of that column. ^\’.^I.^I.^I.^W.^.^R.^I.^!.^I.^E.^\’.^I.^-.^!.^I.^I.^!.^].^!.^I.^8.^I.^I.^I.^6.^I.^I.^I.^!.^I.^I.^$.^!.^!.^].^?.^!.^,.^!.^\’.^I.^!.^\.^I.^\.^\’.^I.^9.^I.^!.^9.^J.^I.^..^I.^I.^I.^I.^I.^I.^T.^I.^\.^I.^E.^!.^”.^!.^\.^9.^!.^I.^!.^E.^I.^M.^I.^I.^I.^.^.^!.^.^\’.^!.^R.^I.^].^].^I.^3.^I.^”.^I.^I.^9.^I.^I.^-.^I.^I.^(.^!.^!.^I.^!.^!.^E.^I.^I.^!.^!.^Q.^I.^I.^I. I’m not sure what this means and can’t seem to find anything in the…

Difference between vcf2fq and bcftools consensus 1 Hi everybody, I’m working for generate consensus sequence and I’m interogating myself about the differences of work process between bcftools consensus and vcf2fq from vcfutils.pl. In the one hand, thanks to vcf2fq, I can generate consensus sequence with the following command: bcftools mpileup…

Change sequence ID in fastq file generated by bcftools mpileup 0 Hi everobody ! I’m currently work on a HHV8 genetic study and I face to an issue with my bcftools command. Indeed, I want to generate consensus sequences thanks bcftools mpileup command and bam files. However, all ID get…

How to force bcftools to call all variants 1 Hello I am using bcftools to call variants with this command: bcftools mpileup -Ou -b bamlist -f ref.fasta | bcftools call -Ob -mv >variant.bcf However, for some specific variants that I know to exist (looking at bam files with IGV), I…

How do I call all the variants with BCFTOOLS? 0 Hello I am using bcftools to call variants with this command: bcftools mpileup -B -q30 -Q30 -f reference.fasta -a FORMAT/DP,FORMAT/AD –threads 6 -R list_of_specific_position.txt file.bam | bcftools call -m -f GQ -O v -o call_variant.vcf For some specific variants that…

How can I use bcftools mpileup or an alternative to find ALL variants without any probabilistic inference? 0 Hello! I have a pipeline for a maximum depth sequencing project. Briefly, this means I can ignore PCR errors because I check for consensus of UMI-tagged sequences. Therefore, once I have a…

Hi everyone, Recently, I have been using bcftools consensus to generate consensus sequence as the following commands: bcftools mpileup -Ou -f ref.fa in.bam | bcftools call -Ou -mv –ploidy 1 | bcftools norm -f ref.fa -Oz -o norm.vcf.gz bcftools index norm.vcf.gz bcftools consensus -f ref.fa -o consensus.fa norm.vcf.gz However, the…

BCFtools for somatic vs. germline variant calling 0 Hi there, I have seen the workflow ‘mpileup > call’ using BCFtools discussed in the context of both germline and somatic variant calling. It’s not clear to me, then, how the program differentiates between the two. If I’m seeking to identify strictly…

how to get to a VCF from bam files 0 Hello, My situation is as follows: I have two groups of reads/Individuals that differ in terms of indels (one group has the indels, the other doesn’t). I already Mapped them and generated bam files. So, now I am struggling to…

Problem generating a .vcf after upgrade of samtools and bcftools 1 Hi I used to go over candidate sites of variation using SAMtools mpileup after which I used to execute some evaluations of the data using BCFtools. In general I used to provide the reference fasta genome and use the…

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…

samtools mpileup – bases string explanation 0 Hi, I am trying to understand the samtools mpileup bases string output and I am having problems with: ^ (caret) marks the start of a read segment and the ASCII of the character following `^’ minus 33 gives the mapping quality $ (dollar)…

Calling with samtools mpileup calls fewer SNPs than expected. 0 Hello, I’m master course student, and I’m embarrased that I’m very poor at controlling bam files and samtools I tried to variant_calling with samtools mpileup, but as a result, I got a few SNPs (fewer SNPs than expected) As you…

Samples RNA-seq We used the same publicly available data source of human post-mortem brain samples as Van Booven et al.7, which were collected from the New South Wales Brain Tissue Resource Center. Van Booven et al.7 also performed differential splicing, but they used different methods, included individuals from disparate ancestral…

Chromosome “whole genome shotgun sequence” not found 2 Hello everyone, I hope that you´re okay Today I’m trying to do an analysis with population 2 but before I have to bind my .bam files using mpileup. The problem is that when I try to bind the .bam files using mpileul…

reference for freebayes or samtools mpileup after extracting chromosome from alignment 1 Good evening, I have extracted one chromosome from alignment map (.bam), using samtools view: samtools view -b map.bam chr1 > map_chr1.bam Now I would like to perform SNP calling using freebayes. Is it correct to use chr1.fasta as…

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Error: Building DAG of jobs… WildcardErrorin line 502 of /path/to/pipeline/workflow/Snakefile.py: Wildcards in input files cannot be determined from output files: ‘anc_r’ Code: import os import json from datetime import datetime from glob import iglob # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Define Constants ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # discover input files using path from run config SAMPLES…

reference for samtools mpileup after extracting chromosome from alignment 0 Good evening, I have extracted one chromosome from alignment map (.bam), using samtools view: samtools view -b map.bam chr1 > map_chr1.bam Now I would like to prepare file for SNP calling using samtools mpileup. Is it correct to use chr1.fasta…

Hello everyone, I am trying to get genotype likelihoods using bcftools. I am using bcftools version 1.11, running bcftools mpileup and bcftools call. This is what I run: bcftools mpileup -d 8000 -Ou -f $reference $input | bcftools call -mv -Ob -o $variants However, when I check the columns INFO…

Hello, I am working with whole genome resequencing data from non-reference organisms. I am working with low-to-medium depth data (8X-20X) and as expected, there is a bias towards the reference allele during mapping and genotype calling. I have now encountered several scenarios where this bias overwhelms biological signal and misleads…

How does one interpret the quality score in the FASTQ (or BAM) results coming out from the Illumina Novaseq 6000 Sequencer and DRAGEN pipeline. Any ideas or pointers? Occur ASCII ASC-to-Num PHRED Q value? 82 * (42-33) or 9 Q10? Q0? 65 5 20 152 7 22 37377 : (58-33)…

How can I creating multisample VCF file ? 0 Hello, I want to create a multisample VCF file. I have bam files from various alignment. I ran the command bcftools mpileup -d 100000 -f ~reference *.bam | bcftools call -c > concate.vcf Is this step scientifically correct? Or do I…

Sample collection We obtained the short read sequences for 33 brown bear genomes, four polar bears (Ursus maritimus) and two American black bears (Ursus americanus), publicly available from NCBI’s SRA repository (Table S1 and Fig. 1a)12,13,15,16,40,51,65. Next, we selected from our private collections a total of 95 additional samples for sequencing, among…

find tandem repeats in DNA from CRAM/VCF file 0 I want to find tandem repeats in DNA. I have access to CRAM file and the VCF file. I initially tried to get the insertions from the VCF file, but I am not sure if the variant caller has included all…

Change sample ID in BAM file to cell barcode 0 Hi all. I have a BAM file from one 10X scRNAseq sample. I want to try a tool out which was designed for a different type of data. The input for this tool is the output from samtools mpileup. samtools…

samtools calmd and original base quality 0 Hi, I’m currently trying to use samtools calmd to calculates MD and NM tags for my bam files, I noticed that the typical usage mentioned in the documentation (www.htslib.org/doc/samtools-calmd.html) is samtools calmd -bAr aln.bam > aln.baq.bam and the params -b -A -r means：…

Issue Title State Comments Created Date Updated Date How to get a specific chromosome open 1 2022-07-14 2022-07-18 tabix returns row from VCF file multiple times open 4 2022-07-11 2022-07-18 Modified base parsing failure failure closed 0 2022-07-01 2022-07-18 extract genotype information open 1 2022-06-24 2022-07-18 sam_hdr_remove_lines is inefficient if…

Within analysis, low-coverage whole-genome sequencing out of cfDNA was held to examine blood plasma away from patients with spine metastasis An analysis pipe is made and you will verified to evaluate the brand new CNV condition within the cfDNA, in order to determine whether brand new CIN score, that has…

I would like to calculate sequencing coverage for a WGS project. Both long and short reads. I’ve used samtools as following: samtools mpileup -Q 1 -aa illumina_sorted.bam nanopore_sorted.bam > depth.txt Previously, when I used samtools depth instead, I only had the columns I was interested in (chromosome name / base…

using ANNOVAR annotation clinvar database out wrong position 0 Hello Biostars, I was trying to annotate the VCF using ANNOVAR,but I get a wrong out ,it seems my clinvar database is not sutibale bcftools_callCommand=call -m -v -o /project/plantform/20220316PCR/03.amplify/L2107973CFD7G5kxT1/L2107973CFD7G5kxT1.variation.vcf /project/plantform/20220316PCR/03.amplify/L2107973CFD7G5kxT1/L2107973CFD7G5kxT1.mpileup.vcf clinvar ANNOVAR • 34 views Read more here: Source link

samtools mpileup error – 1 samples in 1 input files 0 Hi All, I have relatively new to bioinformatics and have encountered an issue when trying to generate an mpileup file with samtools. I have entered the following command samtools mpileup -f /home/path_to_reference/nCoV_Jan31.fa.fasta sorted_sample1.sam > sample.mpileup The message returned is…

How to call LOH with FreeC 0 Good morning, I am try to infer loss of heterozygosity (LOH) from WGS data using Freec. For this purpose, I am using these parameters in the “[BAF]” section of the configuration file: [BAF] makePileup = My_somaticVCF.vcf.gz fastaFile = hg19.fa SNPfile = hg19_snp142.SingleDiNucl.1based.txt.gz When…

Removing reads which map to certain region of reference 0 I have mapped reads to a reference genome of a related species. I want to remove reads which map to a specific region (chromosome) of the reference, but I don’t know what the best way to go about it is….

Hi everyone! I have a query regarding variant calling from a high coverage site on the basis of the maximum likelihood variant. I have RNA-seq data mapped bam file. I called variant using the below command. “bcftools mpileup –max-depth 10000 -Oz -f ref.fa sample.bam | bcftools call -mv -Oz -o…

Extreme environments present profound physiological stress. The adaptation of closely related species to these environments is likely to invoke congruent genetic responses resulting in similar physiological and/or morphological adaptations, a process termed “parallel evolution” (1). Existing evidence shows that parallel evolution is more common at the phenotypic level than at…

VCF samtools 0 Hello, I am having trouble when doing variant calling with samtools. I am getting only the header an no variants. If I would instead use Freebayes, I do get a lot of variables, and with Gatk, I get just a few. What can the problem be? Do…

Organoid culture of small intestinal cells and lentiviral transduction C57BL/6J mice and BALB/cAnu/nu immune-deficient nude mice were purchased from CLEA Japan (Tokyo, Japan). The small intestine was harvested from wild-type male C57BL/6J mice at 3–5 weeks of age (Additional file 1: Figure S9A). Crypts were purified and dissociated into single cells,…

INTRODUCTION Large-scale annual migrations occur in an extraordinary range of animals, from insects to the great whales. While the driving mechanisms of these migrations are varied and sometimes poorly understood, they often represent a way of optimizing conditions for breeding and adult fitness when these are in conflict. Often, populations…

samtools mpileup fail to create bcf 1 I have indexed my reference.fasta using bowtie2: bowtie2-build reference.fasta reference.fasta created the bam file form the sam file using samtools, sorted and indexed the bam file: samtools view -S -b Sample1_mapped.sam > Sample1_mapped.bam samtools sort Sample1_mapped.bam -o Sample1_sorted > Sample1_sorted.bam samtools index Sample1_sorted.bam…

phase_trio.sh | searchcode PageRenderTime 24ms CodeModel.GetById 16ms app.highlight 5ms RepoModel.GetById 1ms app.codeStats 0ms /Phase/phase_trio.sh github.com/BioinformaticsArchive/fCNV Shell |…

Bcftools how to add DP to FORMAT field (get per sample read depth for REF vs ALT alleles ) 1 I’m trying to achieve what this post was looking for Add Dp Tag To Genotype Field Of Vcf File Currently this is my command: bcftools mpileup -Ou –max-depth 8000 –min-MQ…

Vcfutils error code 20-08-2021 code at line (I think) just to get it to write a proper fq. Second issue is this error: substr outside of string at /usr/local/bin/object91.ru line We can do this in a single…

Calling variants on reads with MAPQ=0 on HaplotypeCaller or bcftools mpileup 2 I am working with about 500 samples of human exome data. used hg19 to align my reads and ran a standard best-practices GATK workflow. Later only to realise that a small 1Mb loci has not mapped properly due…

EOF marker absent in VCF – can this be safely ignored? 0 Hi, I generated a VCF file using a bcftools mpileup | bcftools call pipeline. I have done this before, and the file produced then looks fine. However, the log for this one had [W::bgzf_read_block] EOF marker is absent….

bcftools consensus still returns “Could not parse the header” error 0 I attempted to create a consensus fasta file using bcftools, i.e. bgzip -c All_SRR_SNP_Clean.vcf > All_SRR_SNP_Clean.vcf.gz tabix All_SRR_SNP_Clean.vcf.gz cat $ref| bcftools consensus $vcf_dir/All_SRR_SNP_Clean.vcf.gz > consensus.fasta where $ref is the path to a Drosophila reference genome fa and the vcf…

Extremely low number of variants in VCF file after filtering MIN(FORMAT/DP)>10 0 I’m doing microbiome analysis where I’m looking for SNPs in a large number of microbe species’ genomes. I ran my bcftools pipeline on around 15 bacterial and viral species from which the end result produced a number of…