Missing reference allele in GVCF file after running HaplotypeCaller
Hi, I used HaplotypeCaller in GVCF mode to generate a single sample GVCF, but when I checked my vcf file I see that the reference allele is not showing up: 22 1 . N <NON_REF> . . END=16050022...
View ArticleDifferences between BQSR pipeline in two different GATK documents
Hi, I noticed that the pipeline for BQSR is slightly different between the "Workshop walkthrough (Brussels 2014)" document and the "(howto) Recalibrate base quality scores = run BQSR" document. I used...
View ArticleBest Practices VQSR parameters updated
The Best Practices recommendations for Variant Quality Score Recalibration have been slightly updated to use the new(ish) StrandOddsRatio (SOR) annotation, which complements FisherStrand (FS) as...
View Articlegenotype calling in gatk
Excuse me: After calling the genotype using Haplotyper Caller in gatk, i manually check the reads covering the variant sites. But i found one exception: The genotype of one sample was 0/0，wild type,but...
View ArticleCombineGVCFs - All alleles are missing
Hi, I am combining gcvf files into single gvcf files by chromosome, using CombineGVCFs, in order to run GenotypeGVCFs. When I checked the first gvcf file generated by CombineGVCFs, I noticed that at...
View ArticleRegistration open for GATK workshop (March 19-20)
Registration is now LIVE for our upcoming BroadE Workshop: Best Practices for Variant Calling with the GATK. WHEN: Thursday, March 19 & Friday, March 20, 2015 10:00 AM - 5:00 PM (Lecture, March 19)...
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Mini Workshop (ASHG) 2014 Oct 21: Best Practices for Variant Discovery with GATK
Ami Levy-Moonshine presented this condensed 90-minute workshop given at ASHG 2014 in San Diego, CA on October 21. This workshop covered all the core steps involved in calling variants with the GATK,...
View ArticleGATK VQSR tranches
Hi all - I'm stumped and need your help. I'm following the GATK best practices for calling variants with HaplotypeCaller in GVCF mode. One of my samples is NA12878, among 119 others samples in my...
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Best Practice pipeline for WES, including VQSR - what is best?
I am currently processing ~100 exomes and following the Best Practice recommendations for Pre-processing and Variant Discovery. However, there are a couple of gaps in the documentation, as far as I can...
View ArticleWorkshop presentations -- 2015 UK 4/20-24
The presentation slides from the 2015 "GATK in the UK" workshop (April 20-24) are available on DropBox here. All slides will ultimately be posted in the Presentations section of the Guide.
View ArticleUnusual calls after using HaplotypeCaller - filtered with VQSR and refinement...
Hi, I have discovered some unusual calls in my VCF file after using HaplotypeCaller. I am using version 3.3 of GATK. I applied VQSR as well as the genotype refinement workflow...
View ArticleBest practice for variant calling on Ion Torrent data with GATK
Hi, I wonder how well GATK works with Ion Torrent data. Is there any recommended practice to handle Ion Torrent data, especially SNP and indel calling, with GATK? Thanks, XZ
View ArticleRealigning sample-merged bam files?
Following GATK's best practices, I have individually realigned/recalibrated my sample-lane bams and merged them by sample: sample1_lane1.dedup.realn.recal.bam --> sample1_lane2.dedup.realn.recal.bam...
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Best Practices for Variant Discovery in DNAseq
This article is part of the Best Practices documentation. See http://www.broadinstitute.org/gatk/guide/best-practices for the full documentation set. This is our recommended workflow for calling...
View ArticleWhen to use BQSR?
Hi, I am new to NGS/GATK & have a paired-end targeted (targeted to 1 region on 1 autosome) illumina sequencing project on roughly 470 samples. I was wondering whether Indel Realignment & BQSR...
View ArticleBQSR on single samples or merged BAMs
Hi, I have ~150 WGS all sequenced in batches on Illumina HiSeq over a number of years, on a number of machines/flowcells. I want to perform BQSR on my BAM files before calling variants. However for my...
View ArticleGATK usage for Targetted Exome sequencing data analysis
We are using a licensed version of GATK here. The version is GATK version -2014.3-3.2.2-7-g f9cba99. While using the tool for analysis of exome data I had few questions. 1: Are there different...
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Away Workshop (Philadelphia) 2014 Sep 18-19: Best Practices for Variant...
Eric Banks, Sheila Chandran and Geraldine Van der Auwera presented this workshop in Philadelphia, PA, upon invitation from the School of Medicine at UPenn. This workshop covered all the core steps...
View ArticleGenotypeGVCFs
I was trying to do combine sets of vcf files for all my samples so that I have one single vcf output using this command option below java -d64 -Xmx48g -jar ${GATK}/GenomeAnalysisTK.jar \ -R ${REF} \ -T...
View ArticleCancer variant calling workflow with mutect and changes/additions to the GATK...
Hi all, I'm working on a cancer variant calling workflow (DNAseq) with MuTect as the variant caller, rather than HaplotypeCaller (due to it's low AF intolerance). I've gone through the forum and...
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