CollectVariantCallingMetrics varies depending on version of b37 DbSNP
Please review the questions I posted at https://gatkforums.broadinstitute.org/gatk/discussion/10041/varianteval-error-message#latest. They appear as "Answered" but are in fact not. Thanks.
View ArticleGenotypeGVCFs multiple gvcf bug
Hi all - I've tried using the GenotypeGVCFs in both 3.7 and 4.0, but get different errors in each. for 3.7 (nightly-2017-05-17-g44b6fa2). I get: java -Xmx124g -jar ~/bin/gatk/GenomeAnalysisTK.jar -T...
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Unboxing GATK4
This is one of two posts announcing the imminent beta release of GATK4; for details about the open-source licensing, see this other post. You've probably heard it by now: we are on the cusp of...
View ArticleAnalyzeCovariates error (R)
Hello I am trying to generate a base recalibration plots using AnalyzeCovariate My command is such java -jar GenomeAnalysisTK.jar \ -T AnalyzeCovariates -R GRCh37-lite.fa \ -before...
View ArticleDoes Picard PF_MISMATCH_RATE metric include both mismatch and indel?
I wonder do the Picard (CollectAlignmentSummaryMetrics) PF_MISMATCH_RATE and PF_HQ_ERROR_RATE metrics include both mismatch and indels? Or they only calculate the number of mismatched bases (e.g. error...
View Articlequestions about downsampling
Hi, I am using HaplotypeCaller to call variants on targer region sequencing data, the mean coverage is about 600, I want to downsample my data to test the minumum mean coverage required for variant...
View Article-maxAltAlleles argument ignored in HC and genotypeGVCFs in GATK-3.7?
Hi there I have a similiar issue as described here: http://gatkforums.broadinstitute.org/gatk/discussion/5111/haplotypecaller-pooled-sequence-problem I am using GATK version 3.7-0-gcfedb67 on poolseq...
View ArticleOncotator error message
Hello, I've installed oncotator/1.5.1.0 and try to run it with python/2.7.3 on my vcf files with the following command line: oncotator -i VCF --db-dir ./oncotator_db -o VCF mutect.vcf annotated.vcf...
View ArticleGATK v4 Variant Recalibrator command line
Could someone please provide me with a sample command line to run Variant Recalibrator for GATK v4? I am running the tool using GATK 4 Alpha with the following command line:...
View Articlerunning gatk snp call in KNL computing node (Intel Xeon Phi 7250)
Hi there, I would like to run gatk SNP call in TACC stampede2 machine (https://portal.tacc.utexas.edu/user-guides/stampede2) and they have the KNL node equipped with Intel Xeon Phi 7250. This CPU is...
View ArticleProblem with HaplotypeCaller and GenotypeGVCFs
Hi just wondering if you have any experience with this problem. I am following GATK best practices for a targeted sequencing experiment. After the GenotypeGVCFs phase the majority of variants are...
View ArticleMaking GATK available on the cloud for everyone
Today, several members of our extended group are talking at the BioIT World meeting in Boston, and the Broad mothership is putting out a handful of announcements that are related to GATK. Among other...
View ArticleHeterozygous X variants observed in male samples called by HaplotypeCaller in...
Hello GATK team, I have called variants with HaplotyeCaller in the whole exome data of 6 people (4 affected males and 2 unaffected). All 4 male patients are heterozygous for three variants in a gene...
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(How to) Map reads to a reference with alternate contigs like GRCh38
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. This exploratory tutorial...
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DP differences between haploid and diploid mode
I would appreciate some help in understanding better the differences between haploid and diploid mode when it comes to calling and joint-genotyping (HaplotypeCaller + GenotypeGVCFs) in gatk. In...
View ArticleUsing GenomicsDBImport to prepare GVCFs for input to GenotypeGVCFs in GATK4
In GATK4, the GenotypeGVCFs tool can only take a single input, so if you have GVCFs from multiple samples (which is usually the case) you will need to combine them before feeding them to GenotypeGVCFs....
View ArticleRelease notes for GATK version 3.8
GATK 3.8 was released on July 28, 2017. Itemized changes are listed below. For more information on what you should care about, see the user-friendly version highlights (coming soon). Performance...
View ArticleVersion highlights for GATK version 3.8
One more 3.x version, for the road! That's right, even as we're ramping up our efforts on GATK4 (we're three beta releases in at this point, and getting down to brass tacks writing the migration guide...
View ArticleIs 70k millions variants for WES trios enough?
Hi there, I am using GATK for trio analysis of WES data where I have proband and parents. I would like to execute a Joint analysis of all the 50 families that I have but could not get more than about...
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