GATK 3.7 HaplotypeCaller out vcf format
Hi everyone, I just want to confirm what I got back from HaplotypeCaller (GATK 3.7) is correct format, it is VCF4.2 format, however, after following the best practice, I have a vcf file with the GT...
View Article(howto) Call variants with HaplotypeCaller
Objective Call variants on a single genome with the HaplotypeCaller, producing a raw (unfiltered) VCF. Caveat This is meant only for single-sample analysis. To analyze multiple samples, see the Best...
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(howto) Discover variants with GATK - A GATK Workshop Tutorial
GATK TUTORIAL :: Variant Discovery :: Worksheet June 2016 - GATK 3.6 This tutorial covers material taught at GATK workshops, and focuses on key steps of the GATK Best Practices for Germline SNP and...
View ArticleGATK and PBS clusters
Dear all, has someone some more experience with running GATK on PBS computer clusters ? We have a PBS cluster at UCSF, and the jobs in GATK3.5 calling IR, BQSR, and MUTECT2 stop for some reason...
View ArticleGATK4-Alpha MarkDuplicates crashing
I've used Picard2.1 MarkDuplicates for a bunch of bam files (4-40x coverage) generated with Picard2.1 MergeSamFiles and it works fine. I'm trying to get GATK4-Alpha MarkDuplicates working on the bam...
View ArticleDramatic decrease in the number of variants discovered after applying --ploidy
Hi! I did two haplotypecaller GVCF runs on DNA-Seq data, one with default ploidy 2 and one with ploidy 28 (my library is a pool of 14 diploid animal samples). I noticed there is a drastic decrease in...
View ArticleLink to download Mutsig 2.0
I am not able to find link on the cgatools site as it only shows MutSigCV1.4 for download. Can someone please provide link to download MutSig2.0?
View ArticleWhat is the difference between QUAL and GQ annotations?
There has been a lot of confusion about the difference between QUAL and GQ, and we hope this FAQ will clarify the difference. The basic difference is that QUAL refers to the variant site whereas GQ...
View ArticleVCF - Combining two columns into one column
I have a VCF file with multiple samples (multiple columns). There are replicate samples. Essentially, I want to combine two columns into one. The GT:AD:DP:GQ:PL data would obviously have to be...
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Base Quality Score Recalibration (BQSR)
BQSR stands for Base Quality Score Recalibration. In a nutshell, it is a data pre-processing step that detects systematic errors made by the sequencer when it estimates the quality score of each base...
View ArticleWhat's in the resource bundle and how can I get it?
NOTE: we recently made some changes to the bundle on the FTP server; see the Resource Bundle page for details. In a nutshell: minor directory structure changes, and Hg38 bundle now mirrors the cloud...
View ArticleRNAseq preferred reference - b37 or hg19?
Hi. I'm wondering if there's a preferred human reference build for aligning RNAseq data? The only factor that even leads me to ask this question is the following article...
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What are the smallest units I can break whole human genomes into, for...
Hi, and thank you so much for the wonderful tools and support! For our current project, we'd like to run 2000+ whole genomes from FASTQ to VCF using GATK best practices. I'd like to optimize the...
View ArticleGATK HaplotypeCaller does not forward @PG BAM header lines to -bamout
Hey GATK Devs! I'm using GATK (v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18) to call SNPs and Indels on a single sample. The reads were aligned with BWA (v0.7.12) and duplicates marked with Picard...
View Articleparallel running in GATK
In HC, CombineGVCFs, and GenotypeGVCFs, besides running each chr separately in parallel, can I also break a chr into smaller sections and run each in parallel? Thanks!
View Articleerror while calling snps for ion s5 samples
I am running GATK for snp analysis on my Ion S5 Samples I am currently using reference file hg19 which i downloaded from gatk resource bundle I am getting this error any help is highly appreciable INFO...
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(How to) Call somatic copy number variants using GATK4 CNV
Presented tools are in BETA. Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section and be sure to read about updates also within the Comments section....
View ArticleWhole Genome Sequencing data analysis
Hello, We are new in whole genome sequencing (WGS) data analysis. Earlier received lots of help and suggestions from GATK team regarding whole exome sequencing analysis and in-house database...
View ArticleOncotator Errno28
I am using oncotator v.1.9.2.0 to annotate a VCF with whole-genome variants from 8 samples. This is the command I am using: oncotator -v -i VCF --skip-no-alt --db-dir $DIR/oncotator_v1_ds_Jan262015...
View ArticleInbreedingCoeff calculation with trio, pairs, singletons etc
Hi Team I plan to filter FPs on a cohort of 200 exomes using VQSR. I understand filtering on InbreedingCoeff is not suitable when family relations are present unless specified in a PED file. My issue...
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