Tag: picard

Hello all, In my NGS workflow for UMI based reads, I first tried identifying and removing sequence adapters using bbmerge and cutcadapt: BBMERGE -Xmx1g -ignorejunk in1=SAMPLE_R1 in2=SAMPLE_R2 outa= adapters.fa itn CUTADAPT -a forward_adapter -A reverse_adapter -o s_2_1_sequence_trimmed_UN.fastq.gz -p s_2_2_sequence_trimmed_UN.fastq.gz SAMPLE_R1 SAMPLE_R2 Then, I converted the trimmed fastq files to an…

Hamblin MT, Di Rienzo A. Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am J Hum Genet. 2000;66:1669–79. Article  CAS  PubMed  PubMed Central  Google Scholar  Hamblin MT, Thompson EE, Di Rienzo A. Complex signatures of natural selection at the Duffy blood group…

The specific environmental/history/collection context The Huseby Klev materials were unearthed and collected by archaeologists (including two of the co-authors of this article) during the excavation of this coastal hunter-fisher-gatherer site in the 90s50. The material assemblage was rich and well preserved: human bones, animal bones, plant remains and pieces of…

Category Sam/Bam Manipulation Usage java -jar picard.jar SetNmMDAndUqTags I=sorted.bam O=fixed.bam \ Manual INPUT (File)    The BAM or SAM file to fix. Required. OUTPUT (File)    The fixed BAM or SAM output file. Required. IS_BISULFITE_SEQUENCE (Boolean)    Whether the file contains bisulfite sequence (used when calculating the NM tag). Default value: false. This option can be…

Mouse brain tissues All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee under protocol number 18-00006. Adult (P56) C57BL/6J male mice were purchased from the Jackson Laboratory at 7 weeks of age and maintained in the Salk animal barrier facility on 12-h dark–light…

“Unlock Your Potential: Join AstraZeneca as a Bioinformatics Consultant and Revolutionize Drug Discovery!” –Must See– AstraZeneca Bioinformatics Job Job Post: Consultant – Bio Informatician At AstraZeneca, our mission is to improve the quality of healthcare and make a positive impact on the lives of millions of patients. We are seeking…

Sorted bam files are empty after sorting them from bam 0 Hi, I have been working with all my DNA analysis files in parallels but I got to a point where I had about 15 files get stuck on one step. Specifically, I notice something is wrong because the files…

NOTE: This collection was originally posted at SeqAnswers.com. Creating a copy here to preserve the information.Part I is available here: Yes .. BBMap can do that! – Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)Part II is available here: Yes .. BBMap can…

Palikaras, K., Lionaki, E. & Tavernarakis, N. Mechanisms of mitophagy in cellular homeostasis, physiology and pathology. Nat. Cell Biol. 20, 1013–1022 (2018). Article  CAS  PubMed  Google Scholar  Palikaras, K., Lionaki, E. & Tavernarakis, N. Coordination of mitophagy and mitochondrial biogenesis during ageing in C. elegans. Nature 521, 525–528 (2015). Article …

subset a bam file 1 I possess numerous sorted BAM files; however, for my project, I am required to randomly select a subset of reads (1e5) from them. I have explored the option of converting a pysam object to a list, but encountered issues with substantial memory usage and slow…

Use of IDR after running MACS3 for ATAC-seq data 0 Cross-posted from github (a little worried about the inactivity there; please let me know if this is not good practice) I am analyzing ATAC-seq data from human cells. I am planning to perform the following as part of my pipeline:…

Tartt AN, Mariani MB, Hen R, Mann JJ, Boldrini M. Dysregulation of adult hippocampal neuroplasticity in major depression: pathogenesis and therapeutic implications. Mol Psychiatry. 2022;27(6):2689–99. doi.org/10.1038/s41380-022-01520-y Article  CAS  PubMed  PubMed Central  Google Scholar  Friedrich MJ. Depression is the leading cause of disability around the World. JAMA. 2017;317(15):1517. doi.org/10.1001/jama.2017.3826 Article  PubMed …

I am setting up a Snakemake pipeline for sequencing reads alignment and variants calling. But the samtools index rule is not activated, and the subsequent haplotype caller rule fail. I think it is because the samtools index rule is not perceived as necessary to execute the output of rule all…

Ethic statement The Clinical Research Ethics Review Committee of Kyushu University Hospital approved the study (permit no. 29-43, 30-268, and 700-00). Written informed consent for the current research project was obtained before the tumor tissue, and a blood sample were harvested. This study was also conducted according to the principles…

Roger, A. J., Muñoz-Gómez, S. A. & Kamikawa, R. The origin and diversification of mitochondria. Curr. Biol. 27, R1177–R1192 (2017). Article  CAS  PubMed  Google Scholar  Monzel, A. S., Enríquez, J. A. & Picard, M. Multifaceted mitochondria: moving mitochondrial science beyond function and dysfunction. Nat. Metab. 5, 546–562 (2023). Article  PubMed …

Picard downsample metric file 0 Hello, I am trying to downsample my bam file using picard , using the following command. The documentation states that the Metrics_file is a optional parameter, though its giving me the error , the command I am using is java -jar /home/apps/software/picard/2.10.1-Java-1.8.0_152/picard.jar DownsampleSam I= myinput_unique_rmdup.bam…

Hi! I am having issues for the first time with CombineGVCFs. Specifically, it outputs a combined gvcf without chromosome 8 (SUPER_8) even though this is present in the individual gvcfs that I input in the command. There is no error in the log file, the engine just shuts down after…

!*! GENERAL SUMMARY/ OVERVIEW STATEMENT: In Gulhan Lab, we develop statistical and machine learning methods for cancer genomics to improve patient classification and early cancer detection strategies. We aim to decipher the broad spectrum of genomic instabilities that dictate the evolution of cancer genomes, and to understand how best to…

Sun L, Wu J, Du F, Chen X, Chen ZJ. Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway. Science 2013; 339(6121): 786–791 Article  CAS  PubMed  Google Scholar  Wu J, Sun L, Chen X, Du F, Shi H, Chen C, Chen ZJ. Cyclic GMP-AMP…

Different number of reads when converting data from FASTQ to BAM and CRAM to FASTQ 1 This post is following up on this other question FASTQ to BAM to CRAM to FASTQ. I have developed an NGS pipeline for calling variants from amplicon data. Regarding the backup, we want to…

anilkumar@ak-omen-laptop:~/NGStools/gatk-4.4.0.0$ gatk –java-options “-DGATK_STACKTRACE_ON_USER_EXCEPTION=true” BaseRecalibrator -I “/media/anilkumar/My Passport/CRC/fastq/C_4_mkdp.bam” -R “/media/anilkumar/My Passport/CRC/fastq/hg19.fa” –known-sites “/media/anilkumar/My Passport/CRC/fastq/dbsnp_138.b37.vcf” –known-sites “/media/anilkumar/My Passport/CRC/fastq/Mills_and_1000G_gold_standard.indels.b37.vcf” –known-sites “/media/anilkumar/My Passport/CRC/fastq/1000G_phase1.indels.b37.vcf” -O “/media/anilkumar/My Passport/CRC/fastq/C_4_bqsr.table” Using GATK jar /home/anilkumar/NGStools/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar /home/anilkumar/NGStools/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar BaseRecalibrator -I /media/anilkumar/My Passport/CRC/fastq/C_4_mkdp.bam -R /media/anilkumar/My Passport/CRC/fastq/hg19.fa –known-sites /media/anilkumar/My Passport/CRC/fastq/dbsnp_138.b37.vcf –known-sites /media/anilkumar/My Passport/CRC/fastq/Mills_and_1000G_gold_standard.indels.b37.vcf –known-sites…

The Position Principal Bioinformatics Scientist We are seeking a highly skilled and experienced Principal Bioinformatics Scientist specializing in Next Generation Sequencing (NGS) to join our research team. As a Computational Biologist in NGS, you will lead and contribute to cutting-edge projects focused on analyzing and interpreting NGS data, playing a…

I wish to input the names of my samples in a table with the corresponding files of reads forward and reverse to use them in a Snakemake workflow: sample fq1 fq2 1 ../reads/110627_0240_AC0254ABXX_2_SA-PE-001.1.fq.gz ../reads/110627_0240_AC0254ABXX_2_SA-PE-001.2.fq.gz 2 ../reads/110627_0240_AC0254ABXX_2_SA-PE-002.1.fq.gz ../reads/110627_0240_AC0254ABXX_2_SA-PE-002.2.fq.gz 22 ../reads/110802_0249_AD0CM0ABXX_3_SA-PE-022.1.fq.gz ../reads/110802_0249_AD0CM0ABXX_3_SA-PE-022.2.fq.gz Unfortunately, the management of the wildcards is more complex and…

Does GATK SetNmMdAndUqTags reduces the size of a CRAM? 0 I performed GATK SetNmMdAndUqTags on a CRAM file for Whole Genome Sequencing after completing the MarkDuplicates step. The initial size of the CRAM file was 19GB, and after performing the SetNmMdAndUqTags operation, its size reduced to 8GB. The following is…

About us Our goal is to accelerate innovation in healthcare through partnerships to bring high-quality software solutions and technologies to market. Essential Duties and Responsibilities: Work with bioinformatics SQA engineers and members of a bioinformatics group to develop test cases that ensure the quality of bioinformatics software used in FDA…

Review doi: 10.1186/s13195-023-01322-6. Affiliations Expand Affiliations 1 Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA. 2 Department of Family Medicine, Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX, USA. 3…

2021 Alzheimer’s disease facts and figures – 2021 – Alzheimer’s & Dementia – Wiley Online Library. Available from: alz-journals.onlinelibrary.wiley.com/doi/doi.org/10.1002/alz.12328. [Cited 2022 Nov 13]. Jack CR, Bennett DA, Blennow K, Carrillo MC, Dunn B, Haeberlein SB, et al. NIA-AA research framework: toward a biological definition of Alzheimer’s disease. Alzheimers Dement J…

Picard Liftover MismatchedRefAllele PsychArray 0 New to using liftOver and working with vcf files generally: I ran liftOver on data gathered from the PsychChip array to lift over from GRCh37 to GRCh38, and got only about 50% of variants lifted over. Most of the rejected ones had “MismatchedRefAllele” as their…

Position: Bioinformatics Data Analyst Company: GenomicStar – A SaaS based Precision Medicine Platform Job Purpose: The Bioinformatics Data Analyst will play a critical role in the development, validation, and implementation of data analysis pipelines for various genetic test panels, incorporating state-of-the-art AI techniques. This role is integral to our commitment…

Bosch E, De Vos M, Humaidan P. The future of cryopreservation in assisted reproductive technologies. Front Endocrinol (Lausanne). 2020;11:1–15. Article  Google Scholar  De Geyter C, Calhaz-Jorge C, Kupka MS, Wyns C, Mocanu E, Motrenko T, et al. ART in Europe, 2015: results generated from European registries by ESHRE†. Hum Reprod…

I am trying to make a Snakemake pipeline using a configuration file config.yaml. — samples: – Sample_1: reads/raw_reads_1 – Sample_2: reads/raw_reads_2 – Sample_3: reads/raw_reads_3 reference: – “path/to/reference.fasta” … Following the good practices given in the Snakemake wrapper repository, I have used wrappers commands as much as possible. snakemake-wrappers.readthedocs.io/en/stable/ However I…

How to choose LiftOver chain file 1 I am trying to liftover a hg38 Whole Genome Sequenced VCF to hg19 VCF. Planning to use GATK Picard for this. However not sure which liftover chain file to use from this path: hg38tohg19 picard LiftOver • 32 views • link updated 31…

Dickmann DI, Kuzovkina J. Poplars and willows of the world, with emphasis on silviculturally important species. In: Isebrands JG, Richardson J, editors. Poplars and willows: trees for society and the environment. Wallingford: CABI; 2014. Google Scholar  Imbert E, Lefèvre F. Dispersal and gene flow of Populus nigra (Salicaceae) along a…

Problem with RNAseq MarkDuplicates(Picard) 0 Hi, I’m trying to use GATK to call variant with RNAseq, but I have some question about MarkDuplicates. In MarkDuplicates document: MarkDuplicates(Picard), mentioned “Set READ_NAME_REGEX to null to skip optical duplicate detection, e.g. for RNA-seq or other data where duplicate sets are extremely large and…

The life expectancy of human beings has gradually increased. The average life expectancy of human beings was only about 30 years in the 19th century and increased to about 72 years in 2019 (Riley, 2005; World Health Organization, 2019). Nonetheless, an extended life doesn’t always equate to a healthier one. According to the…

CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM 0 Hi, I have bulkRNAseq dates (12 samples, pair end sequenced) and my pipine was : I performed quality control with FastqQC, Trimmed reads with Trimmomatic Aligned reads to the reference genome with STAR Used Samtools to sort and index the BAM…

Jones EBG, Suetrong S, Sakayaroj J, Bahkali AH, Abdel-Wahab MA, Boekhout T, et al. Classification of marine Ascomycota, Basidiomycota, Blastocladiomycota and Chytridiomycota. Fungal Divers. 2015;73:1–72. Article  Google Scholar  Van den Wyngaert S, Ganzert L, Seto K, Rojas-Jimenez K, Agha R, Berger SA, et al. Seasonality of parasitic and saprotrophic zoosporic…

Source: Youtube.com The era of big data has revolutionized the way we analyze and interpret complex biological systems. In the field of genomics, Chip-Seq (Chromatin Immunoprecipitation Sequencing) data has become a valuable resource for understanding gene regulation and the functionality of the genome. Chip-Seq data provides insights into the binding…

Wallace DC. Mitochondrial genetic medicine. Nat Genet. 2018;50:1642–9. Article  CAS  PubMed  Google Scholar  Nunnari J, Suomalainen A. Mitochondria: in sickness and in health. Cell. 2012;148(6):1145–59. Article  CAS  PubMed  PubMed Central  Google Scholar  Chan DC. Mitochondria: dynamic organelles in disease, aging, and development. Cell. 2006;125(7):1241–52. Article  CAS  PubMed  Google Scholar  Picard…

MeiraGTx is a clinical-stage gene therapy company focused on developing potentially curative, innovative treatments for patients living with serious diseases of significant unmet medical need.   We are seeking a motivated, enthusiastic, well-rounded individual with experience in computational biology, multi-omics data integration and/or genomics data analysis be a part of…

Liftover GRCh37 to hg38 1kg/GATK. 1 I need to liftover a few variants from GRCh37 to hg38 1kg/GATK. UCSC lifover does not have this reference genome version available. I have tried with the standard hg38 but conversations are wrong. Where can I find GRCh37 to hg38 1kg/GATK chain files or…

Problem while working with sequenza – Chromosomes out of order 1 Hi, I’m trying to work with sequenza in order to calculate HRD score of a sample using WES data. When I run sequenza, I get a message saying that “chromosomes are out of order”, and I don’t know how…

Bacterial strains and growth conditions for eBW1 B. subtilis 168 and E. coli (MG1655) were streaked out from a frozen glycerol stock onto an LB plate and grown overnight at 37 °C. Following a night of growth, a single colony was picked and inoculated into 5 ml of LB broth and grown…

I doing the alignment of samples following the GATK pipeline, and doing the MergeBamAlignment,like this: MergeBamAlignment -ALIGNED $path/file.unsorted.bam -UNMAPPED $path/file.unmapped.bam -O $path/file.merged.bam -R $references/GRCh38.primary_assembly.genome.fa -SO coordinate -TMP_DIR $path/tmp/ i got this error: Exception in thread “main” java.lang.IllegalArgumentException: Do not use this function to merge dictionaries with different sequences in them….

UKB The UKB is a population-based prospective cohort study of more than 500,000 subjects. More detailed information on the UKB is given elsewhere34,35. The study received ethics approval from the North West Multi-center Research Ethics Committee. All participants signed written informed consent before participating. WES data for 450,000 subjects were…

General Summary & Overview StatementThe Iafrate Lab conducts pioneering research in the field of clinical genomics, working to develop personalized approaches to early cancer detection, diagnosis, and therapy. We are seeking a highly motivated bioinformatician with a background in statistics and/or software development to be a part of our team…

BAM 2 FASTQ using Picard and Samtools 0 Hey! Could use some insights, I am changing my BAM 2 fq to align to a new genome and I wanted to make sure I extract the R1, R2 and unmapped reads, so I can use to re-align to new genome. I…

Mouse strains and procedures All animal procedures for this study were approved by the Institutional Animal Care and Use Committee (IACUC) at Duke University (protocol number A215-20-11 was approved on November 9, 2020). All methods were performed in accordance with the relevant guidelines and regulations. The study is reported in…

From VCF to AVINPUT 0 I have VCF files and with the help of this bash script, I am trying to convert them to avinput file type to process faster during annotation process. But strange thing is when the conversion is complete, the number of variants increases. There are more…

Clarification on Sequence Duplication Levels and Qualimap Estimated Duplication Rate 0 Hello, I’m working with illumina paired-end reads. I have merged the data of 2 different runs of the same sample, in order to increase coverage depth. Firstly, I removed duplicates using picard MarkDuplicates: java -jar picard.jar MarkDuplicates \ INPUT=input.bam…

Mahan AL, Ressler KJ. Fear conditioning, synaptic plasticity and the amygdala: implications for posttraumatic stress disorder. Trends Neurosci. 2012;35:24–35. Article  CAS  PubMed  Google Scholar  Koenigs M, Grafman J. Posttraumatic stress disorder: the role of medial prefrontal cortex and amygdala. Neuroscientist. 2009;15:540–8. Article  PubMed  PubMed Central  Google Scholar  Nemeroff CB, Vale…

Salmon error (ex. transcript id appears in the BAM head, but was not in the provided FASTA file) 1 Hello. everyone I am trying to count aligned reads using Salmon in alignment-based mode. My command is: salmon quant -t transcript.fa -l A -a aligned_result.bam -o salmon_quant I am encountering the…

GATK GetPileupSummaries Java heap space 1 I am using GATK GetPileSummaries in the following way: GENOME=”/FILES/HUMAN_REFERENCES/hg19.fa” RECBAM=”/FILES/${patient_id}/${patient_id}.recalibrated.bam” intervals_list=”/FILES/HUMAN_REFERENCES/wgs_calling_regions.v1.interval_list” GERM=”/FILES/HUMAN_REFERENCES/small_exac_common_3-hg19.vcf” PON=”/FILES/HUMAN_REFERENCES/Mutect2-WGS-panel- b37-hg19.vcf”export GERM=”/FILES/HUMAN_REFERENCES/af-only-gnomad-hg19.raw.sites.vcf” VCF=”/FILES/${patient_id}/${patient_id}.recalibrated.vcf” OUTPUT=”/FILES/${patient_id}/${patient_id}.getpileupsummaries.table” srun /mnt/beegfs/apptainer/images/gatk4.sif gatk GetPileupSummaries \ -I $RECBAM \ -L $GERM \ -O $OUTPUT \ -V $GERM Resulting in the following error: 16:37:40.248 INFO NativeLibraryLoader – Loading…

GATK GetPileUpSummariesUsage 0 Hi, I am doing variant calling using as reference hg19. After Gatk Mutect with PON Mutect2-WGS-panel-b37.vcf transformed into Mutect2-WGS-panel-b37-hg19.vcf and germline af-only-gnomad.raw.sites.vcf to af-only-gnomad.hg19.raw.sites.vcf (with Picard LiftOver). After doing Mutect2 next step is GATK GetPileUpSummaries, that has this usage from GATK website: gatk GetPileupSummaries \ -I tumor.bam…

Hi! I am applying Mutect2 in tumor-only.mode having hg19 as reference and samples resulting of targeted sequencing (not only coding gene parts but also some non coding regions), I found this: console.cloud.google.com/storage/browser/gatk-best-practices/somatic-b37%2F;tab=objects?prefix=&forceOnObjectsSortingFiltering=false. This bundle is used for b37 which is equivalent to hg19 (not 100% similar). export PON=”/filepath/Mutect2-WGS-panel-b37-hg19.vcf” export GERM=”/filepath/af-only-gnomad-hg19.raw.sites.vcf”…

Convert files made for b37 into hg19 human reference? 1 Altough hg19 and b37 being considered similar they have some differences that affect the pre processing when doing variant calling. Is there any tool to convert the references for panel of normals or know-sites that are applied in Mutect for…

FilterVcf (picard 2.10.9-1-gaa8c979-SNAPSHOT API) JavaScript is disabled on your browser. @DocumentedFeature public class FilterVcf extends CommandLineProgram Applies a set of hard filters to Variants and to Genotypes within a VCF. Field Summary Fields inherited from class picard.cmdline.CommandLineProgram COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY…

The PositionPrincipal Bioinformatics ScientistWe are seeking a highly skilled and experienced Principal Bioinformatics Scientist specializing in Next Generation Sequencing (NGS) to join our research team. As a Computational Biologist in NGS, you will lead and contribute to cutting-edge projects focused on analyzing and interpreting NGS data, playing a pivotal role…

AdapterMarker (picard 2.10.9-1-gaa8c979-SNAPSHOT API) JavaScript is disabled on your browser. java.lang.Object picard.util.AdapterMarker public class AdapterMarker extends java.lang.Object Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords. This is a very compute-intensive process, so this class implements two heuristics to reduce computation: – Adapter sequences are truncated,…

Cell culture HCC2429 cells were a kind gift from the Hamon Center for Therapeutic Oncology Research at UT Southwestern Medical Center. The cells were grown in RPMI 1640 medium (Thermo Fisher Scientific, #11875119) with addition of 10% heat-inactivated Fetal Bovine Serum (Thermo Fisher Scientific, #10-438-026) and 1% penicillin—streptomycin (Thermo Fisher…

Hello, I have a sorted.bam resulting of targeted sequencing of a set of genes sent to me. When I run Picard AddOrReplaceGroups or Picard MarkDuplicates, I noticed that the order of the chromossomes was not sorted. INFO 2023-07-24 10:39:16 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000:…

Read groups in RNA-seq 0 Hi bioinformaticians, If I have paired end reads for my samples and I am looking to perform alignment either using HISAT2 or STAR, will the alignment results change significantly depending on whether the reads are separately aligned based on read groups (merged subsequently), or if…

Filtering unmapped reads from BAM files 0 I am applying the GATK best practices for variant calling pipeline. By applying the picard addOrReplaceReadGroups I got the error: “invalid_mapping_quality”, I read the post Final Solution For “Mapq Should Be 0 For Unmapped Read.”. So decided to remove unmapped reads with samtools…

SHIFT: Day (United States of America) Bioinformatics Engineer III – Children’s Hospital of Philadelphia (Philadelphia, PA): Lead the data integrity and bioinformatics data analysis of enterprise-level projects in the Center for Data-Driven Discovery in Biomedicine (D3b). Duties include: lead a bioinformatics data operational team responsible for the main bioinformatics analysis…

Dark, P. & Gent, H. Pests and diseases of prehistoric crops: a yield ‘honeymoon’ for early grain crops in Europe? Oxford J. Archaeol. 20, 59–78 (2001). Article  Google Scholar  Mira, A., Pushker, R. & Rodriguez-Valera, F. The Neolithic revolution of bacterial genomes. Trends Microbiol. 14, 200–206 (2006). Article  CAS  PubMed …

GATK not working when clone to VM 0 I has successfully installed gatk for a long time on my computer. Now I got a workstation and cloning it to ubuntu server VM. However, when run the testing with MarkDuplicatesSpark it does not worked like on my computer. This is the…

ReplaceSamHeader (picard 2.10.9-1-gaa8c979-SNAPSHOT API) JavaScript is disabled on your browser. Field Summary Fields  Modifier and Type Field and Description java.io.File HEADER  java.io.File INPUT  java.io.File OUTPUT  Fields inherited from class picard.cmdline.CommandLineProgram COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY Method Summary Methods inherited from class picard.cmdline.CommandLineProgram customCommandLineValidation,…

King, M. C. & Wilson, A. C. Evolution at two levels in humans and chimpanzees. Science 188, 107–116 (1975). Article  ADS  CAS  PubMed  Google Scholar  Konopka, G. et al. Human-specific transcriptional networks in the brain. Neuron 75, 601–617 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Liu, X. et al….

Ethics We confirm our research complies with all relevant ethical regulations and was approved by the animal ethics committee of the School of Biology at the University of St Andrews on 26 July 2018 www.st-andrews.ac.uk/research/environment/committees/awerb/. The three new contemporary dolphin samples analysed in this study were collected under the relevant…

Formenti, G. et al. The era of reference genomes in conservation genomics. Trends Ecol. Evol. 37, 197–202 (2022). Article  CAS  PubMed  Google Scholar  Lee, H. et al. Third-generation sequencing and the future of genomics. bioRxiv, 048603 (2016). Irestedt, M. et al. A guide to avian museomics: Insights gained from resequencing…

< We are seeking a highly motivated postdoctoral candidate with formal training in Bioinformatics, Statistical Genetics, Data Science, or Genetic Epidemiology. A postdoctoral position is immediately available to work on multiple NIH-funded projects on the Genetic Epidemiology of  Alzheimer’s Disease. Projects include: (1) a large scale Mexican-American cohort; (2) families…

Trust in BQSR for AVITI 1 How much can I trust the BQSR quality values? I aligned PE150 data with BWA-MEM, removed duplicates (PICARD). Then I followed this invocation regarding know-sites. I did not use the IndelRealigner (will try this also). I used this on AVITI data for a technical…

Bacterial strains and culture conditions Escherichia coli strain DH5α (Thermo Fisher) was used for the propagation of plasmids, whereas E. coli BL21 DE3 (Novagen) was used for the expression and purification of ResR/McdR protein. Mtb Erdman was obtained from Dr. Ramandeep Singh at THSTI, India, and Mtb H37Rv mc2 790242…

DbSnpBitSetUtil (picard 2.10.9-1-gaa8c979-SNAPSHOT API) JavaScript is disabled on your browser. java.lang.Object picard.util.DbSnpBitSetUtil Nested Class Summary Nested Classes  Modifier and Type Class and Description static class  DbSnpBitSetUtil.DbSnpBitSets Little tuple class to contain one bitset for SNPs and another for Indels. Constructor Summary Constructors  Constructor and Description DbSnpBitSetUtil(java.io.File dbSnpFile, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary) Constructor that creates…

RawWgsMetrics(htsjdk.samtools.util.IntervalList intervals, htsjdk.samtools.util.Histogram<java.lang.Integer> highQualityDepthHistogram, htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredDepthHistogram, double pctExcludedByMapq, double pctExcludedByDupes, double pctExcludedByPairing, double pctExcludedByBaseq, double pctExcludedByOverlap, double pctExcludedByCapping, double pctTotal, int coverageCap, htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredBaseQHistogram, int sampleSize)  Read more here: Source link

Bioinformatics Scientist We are seeking a highly motivated and skilled Bioinformatics Scientist to join our R&D team. The successful candidate will be integral to our genomics research efforts. This role requires expertise building pipelines from sequencer output to feature generation from both RNA and DNA sources. The candidate should have…

Ethics statement This study relied on analyses of genetic data from the UKB cohort, which was collected with informed consent obtained from all participants. Data for this study were obtained under the UKB applications licence number 66995. All data used in this research are publicly available to registered researchers through…

Using bedtools intersect with custom txt files 1 Hi I guess I have a rather simple problem but I couldn’t find a solution in previous answers. From the “COVID19hg” GWAS consortium, I am trying to extract all SNPs that intersect with the coordination of a list of genes I’m interested…

Callaway, E. Oldest Homo sapiens fossil claim rewrites our species’ history. Nature. doi.org/10.1038/NATURE.2017.22114 (2017). Article  PubMed  Google Scholar  Lucas-Sánchez, M., Serradell, J. M. & Comas, D. Population history of North Africa based on modern and ancient genomes. Hum. Mol. Genet. 30(R1), R17–R23. doi.org/10.1093/HMG/DDAA261 (2021). Article  PubMed  Google Scholar  Scerri, E….

Guide to Installing OpenJDK Version 1.8.0_352 on Ubuntu for Picard Tool Compatibility 0 Dear All, I’m looking to download OpenJDK version “1.8.0_352” and install it on Ubuntu so that I can use the Picard tool. However, I’m having trouble finding the download link. Can you please let me know where…

Exome alignment and preprocessing: When I perform an exome alignment, should I use a Ref Genome or Ref Exome .fasta? 1 I’m learning the basis of preprocessing, and I can’t find anywhere a source that would tell me what’s the difference between preprocessing a genome for vc and an exome…

Begier, E. et al. Epidemiology of invasive Escherichia coli infection and antibiotic resistance status among patients treated in US hospitals: 2009-2016. Clin. Infect. Dis. Publ. Infect. Dis. Soc. Am. 73, 565–574 (2021). Article  CAS  Google Scholar  Bélanger, L. et al. Escherichia coli from animal reservoirs as a potential source of…

MeiraGTx is a clinical-stage gene therapy company focused on developing potentially curative, innovative treatments for patients living with serious diseases of significant unmet medical need.   We are seeking a motivated, enthusiastic, well-rounded individual with experience in computational biology, multi-omics data integration and/or genomics data analysis be a part of…

General Summary & Overview StatementThe Iafrate Lab conducts pioneering research in the field of clinical genomics, working to develop personalized approaches to early cancer detection, diagnosis, and therapy. We are seeking a highly motivated bioinformatician with a background in statistics and/or software development to be a part of our team…

GENERAL SUMMARY & OVERVIEW STATEMENT: The Iafrate Lab conducts pioneering research in the field of clinical genomics, working to develop personalized approaches to early cancer detection, diagnosis, and therapy. We are seeking a highly motivated bioinformatician with a background in statistics and/or software development to be a part of our…

If I execute “AddOrReplaceReadGroups” on a sarted and duplicate-marked .bam file, do I have to re-sort and re-mark duplicates? 0 I’m brand new in Bioinformatics, and building my first variant calling pipeline for human genomes. Now, I got stuck using BaseRecalibrator as it needs read groups in my .bam file,…

I’m trying to run Picard CreateSequenceDictionary using the docker image provided by the Broadinstitute (here), but |I’m having troubles when running it, and don’t understand why. I download and run it as: docker pull broadinstitute/picard docker run –rm -v $PWD:/usr/working broadinstitute/picard CreateSequenceDictionary R=ref.fa.gz O=ref.fa.gz.dict But this returns an error: docker:…

Hingorani M, Hanson I, van Heyningen V. Aniridia. Eur J Hum Genet. 2012;20:1011–7. Article  CAS  PubMed  PubMed Central  Google Scholar  Lima Cunha D, Arno G, Corton M, Moosajee M. The spectrum of PAX6 mutations and genotype-phenotype correlations in the eye. Genes. 2019;10:1050. Article  PubMed  PubMed Central  Google Scholar  Cvekl A,…

hardfilter error 0 I got the vcf file without Picard addgroup before making it. but I realized that it was wrong while making hard filter. I did some research and they told me to do a recall bam but I searched and couldn’t find any information about it. Can you…

Building Dict File for GATK 4 I’m going through the instructions page on gatkforums.broadinstitute.org/gatk/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference Specifically, the command I don’t see how to do is: java -jar CreateSequenceDictionary.jar R= Homo_sapiens_assembly18.fasta O= Homo_sapiens_assembly18.dict [Fri Jun 19 14:09:11 EDT 2009] net.sf.picard.sam.CreateSequenceDictionary R= Homo_sapiens_assembly18.fasta O= Homo_sapiens_assembly18.dict [Fri Jun 19 14:09:58 EDT 2009] net.sf.picard.sam.CreateSequenceDictionary done….

sorting BAM file 0 I tried sorting the BAM file i created using gatk-package-4.2.5.0-local.jar SortSam the code is : java -jar gatk-package-4.2.5.0-local.jar SortSam -I {path.bam} -O {path.sorted.bam} -SO coordinate but i encountered this error: INFO: Failed to detect whether we are running on Google Compute Engine. [Tue May 30 16:08:32…

I am trying to run DownsampleSam with Picard version: 2.26.5 on the following script and i get an error about Provider GCS. code: import os,sys from multiprocessing import Pool # the original depth of NA12878 and YH-1 nadepth=812.40 yhdepth=407.25 work_dph=int(sys.argv[1]) napercent = [0.99,0.95,0.90,0.80,0.70,0.60] yhpercent = [0.01,0.05,0.10,0.20,0.30,0.40] #yhpercent = [0.05] NAtotal=”/media/marina/marina2TB/BIOFILES/bams/na.addRG.mdup.bam”…

Hi , I’m trying to do analysis of chipseq data . I have 3 samples Sample1 , sample2 and input I have done QC and then alignment using Bowtie . After that I used samtool to get bam files . Then I have used Picard for duplicate removal. Now I…

Picard’s CollectGcBiasMetrics gc-bias plot- help with interpretation 0 Hi all, Setup I ran picard’s CollectGcBiasMetrics tool for my WES sample, with the intention of assessing the performance of the Exome capture panel in terms of the uniformity of read coverage at various %GC windows. I obtained the gc bias plot…

In breast cancer, the focal amplification of oncogenes plays a critical role in oncogenesis. A recent study published in Nature used whole-genome sequencing (WGS), RNA sequencing, and epigenomic data to identify the underlying mechanism associated with the initiation of focal amplification in breast cancer. Study: ERα-associated translocations underlie oncogene amplifications in breast…

FastQC Function AMPERE quality control tool for elevated throughput sequence data. Your Java What A match Java Runtime Ecology This Picard BAM/SAM Libraries (included in download) Code Maturation Robust. Mature code, but feedback exists comprehended. Code Released No, under GPL v3 or later. Initial Contact Simon Andrews Download Now Views…

hiPSC cell culture and differentiation hiPSCs were maintained on 1:40 matrigel (Corning, #354277) coated dishes in supplemented mTeSR-1 medium (StemCell Technologies, #85850) with 500 U ml−1 penicillin and 500 mg ml−1 streptomycin (Gibco, #15140122). For the differentiation of cortical neurons the protocol described previously21 was followed with slight modifications. Briefly, hiPSC colonies were seeded…

Anderson MJ (2001) A new method for non‐parametric multivariate analysis of variance. Austral Ecol 26(1):32–46 Google Scholar  Anderson MJ (2004) PERMDISP: a FORTRAN computer program for permutational analysis of multivariate dispersions (for any two-factor ANOVA design) using permutation tests. Department of Statistics, University of Auckland, New Zealand, 24. Aykanat T,…

Ethics approval and consent to participate The study was performed in accordance with the Guide for the Care and Use of Laboratory Animals of the US National Institutes of Health (NIH). The Seattle Children’s Research Institute (SCRI) has an Assurance from the Public Health Service through the Office of Laboratory…

Sub-sampling a BAM to a fixed number of reads 0 Hi all, I have recently ben trying to write a simple python script that can produce contaminated synthetic paired end reads for a tool my group are creating. However, in writing this script i’ve been using the following: samtools view…