Release notes for GATK version 2.1
Base Quality Score Recalibration Multi-threaded support in the BaseRecalibrator tool has been temporarily suspended for performance reasons; we hope to have this fixed for the next release. Implemented...
View ArticleFiltering VCF passed to --knownSites or --known on-the-fly?
My current workflow for analysing mouse exome-sequencing (based on v4 of Best Practices) can require me to use slightly different VCFs as --knownSites or --known parameters in BQSR, indel realignment...
View Article"ArithmeticException" in VariantFiltration and "Invalid JEXL expression...
Hi, I have been trying get variants out of a VCF file where the Allele Frequency (AF) is greater than 4%. I have tried both VariantFiltration and SelectVariants but I get different errors with each....
View ArticleSelectVariants and VariantFiltration methods
Hi, I wanted to double check my methods for some targeted capture data. I ran 96 samples through UG to produce a multisample VCF. I separated snps and indels into separate files using SelectVariants,...
View ArticleError when using SelectVariants (affects at least 1.6 - 2.1)
INFO 20:55:27,108 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.1-10-gdbc86ec, Compiled 2012/09/27 05:17:49 INFO 20:55:27,109 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO...
View ArticleRelease notes for GATK version 2.2
GATK release 2.2 was released on October 31, 2012. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history Base Quality...
View ArticleFiltering VCF files
I have used the UnifiedGenotyper to call variants on a set of ~2400 genes (TruSeq Illumina data) from 28 different samples mapped against a preliminary draft genome. I do not have a defined set of SNPs...
View ArticleUsing SelectVariants to output "PASS" records
I have completed filtering my SNP data using VariantFiltration, and now I want to use SelectVariants to output all calls marked "PASS" in the FILTER field. I used the following script, but only the...
View ArticleIn SelectVariants are -conc and -disc complementory in a set-theoretic sence?
I'm looking to find all the entries that change between two calls to UG on the same data. I would like to find all the entries where the call in the variant tract are different from those in the...
View ArticleSelectVariants -number, and missing images from docs....
Hello, I've a couple of essentially documentation-centric questions... Firstly, the SelectVariants documentation describes selecting 1000 random variants from a vcf using '-number 1000', however when I...
View ArticleUpdate of AD field after SelectVariants
Hi, I used the UnifiedGenotyper (GATK 1.6) on a multi-sample set to call variants, and for some of the positions I get multiple mutated alleles. The genotype entries in the combined VCF file look like...
View ArticleSelectVariants: MQRankSum or ReadPosRankSum
Hi, I wouldn't classify this as a bug, but thought I would just put this up here in anyways. I'm creating a vcf file from exome targeted sequencing, using unified genotyper to just call SNVs on one...
View ArticleUsing SelectVariants
SelectVariants SelectVariants is a GATK tool used to subset a VCF file by many arbitrary criteria listed in the command line options below. The output VCF wiil have the AN (number of alleles), AC...
View Articlehow to select a private SNP with GATK from a multisample VCF file
I ran in to the situation now a couple of times that I need to extract a set of private SNPs from a multisample VCF file. For example in a forward genetics knockout screen of a large set of samples. It...
View ArticleCan I use GATK to select a private SNP from multi sample VCF file
Can I use GATK to select a private SNP from multi sample VCF file? With a private SNP I mean a SNP where all but 1 sample in a multi sample vcf file are genotype 0/0.
View ArticleWhat are JEXL expressions and how can I use them with the GATK?
1. JEXL in a nutshell JEXL stands for Java EXpression Language. It's not a part of the GATK as such; it's a software library that can be used by Java-based programs like the GATK. It can be used for...
View ArticleVariantFiltration and SelectVariants
I am trying to filter variant calls which have "GQ>=20.0". GATK SelectVariants, gives no error but gives only the header in the output file java -Xmx2g -jar...
View ArticleProbable bug in SelectVariant --maxIndelSize
Dear All, Just thought I should report a possible small bug with SelectVariant --maxIndelSize as I think it's only filtering insertions greater than the given value and not deletions. Of course using...
View ArticleJEXL and SelectVariants
I'm trying to use JEXL to filter variants but something isn't working and I can't figure it out. I'm hoping someone can point me in the right direction. My VCF file contains an INFO field...
View ArticleSelectVariants
A new tool has been released!Check out the documentation at SelectVariants.
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