Release notes for GATK version 3.1
GATK 3.1 was released on March 18, 2014. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history Haplotype Caller Added...
View ArticleGATK 3.0 HaplotypeCaller RUNTIME ERROR
Hi, I am running Haplotypecaller for ~600 bams to perform gVCF call on a cluster (SGE qsub system). Each node has 32 cores, 256 GB RAM. I am running 8 tasks pernode, so each task has 4 cores and 32GB...
View ArticleI am not sure why HaplotypeCaller does not call my SNV mutation?
Hi Guys, I am using HaplotypeCaller to call mutations for some of patient samples. I know that at MSH2 intron5 near splicing site there is a point mutation in one of the sample. however, this is also a...
View ArticleCombineGVCFs performance
I've got 300 gvcfs as a results of a Queue pipeline, that I want to combine. When I run CombineGVCFs (GATK v3.1-1) this however seems fairly slow: INFO 15:24:22,100 ProgressMeter - Location...
View ArticleHaplotypeCaller '--emitRefConfidence' gives same PL(0) to two genotypes
Hi, In our downstream analysis we have to differentiate between non-variants because of no coverage and confident reference calls. Because of this, we need to pay close attention to HaplotypeCaller...
View ArticleGATK 2.7.4 -mbq and HaplotypeCaller
Dear GATK Team, I am trying to run HaplotypeCaller using GATK 2.7.4. I am getting the following error message: ERROR: Argument with name 'mbq' isn't defined. Here is my command line: java -jar...
View ArticleVCF from GenotypeGVCFs missing fields
So I've just run GenotypeGVCFs and get some odd looking things. The FORMAT field is GT:AD:DP:GQ:PL and on most occasions, the values are 1/1:0,1,0:1:3:10,3,0, i.e. 5 fields. However, sometimes I get...
View ArticleMaximum size for HaplotypeCaller
I'm running HaplotypeCaller, and I was wondering what a recommended cohort size was. Would 30 to 40 families (100 to 150 individuals) be too large? Is there a maximum recommended size for number of...
View ArticleMaximum size for HaplotypeCaller
I'm running HaplotypeCaller, and I was wondering what a recommended cohort size was. Would 30 to 40 families (100 to 150 individuals) be too large? Is there a maximum recommended size for number of...
View ArticleWhat is a GVCF and how is it different from a 'regular' VCF?
This is a placeholder for a document in preparation. Overview GVCF stands for Genomic VCF. A GVCF is a kind of VCF, so the basic format specification is the same as for a regular VCF (see the spec...
View ArticleGenotype and Validate, or Haplotype Caller GGA: what am I doing wrong?
Hi, My use case is quite straightforward, but has been surprisingly hard to achieve: For each sample, I have both Omni 2.5M SNP genotype data and RNA-seq variant call data (done with GATK3). Now I want...
View ArticleReference confidence model (HaplotypeCaller)
This is a placeholder for a document that is under development. For now, please see the document that explains what is a gVCF. That document contains a brief explanation of what is the output of the...
View ArticleDoes HaplotypeCaller use a MAPQ cut-off?
I thought I had seen something in the HaplotypeCaller documentation that said HC didn't look at reads with MAPQs less than 30 by default, and I thought there was a parameter to change this. Was this an...
View Articledetect MNP variants using by Haplotypecaller
Hi! I used Haplotypecaller 3.1 to detect MNP variants. java -Xmx6g -Djava.io.tmpdir=$PWD -jar $GATK -R $hg19 -T HaplotypeCaller -I $bamlist --dbsnp $dpsnp135 -o $call/$sample.all.vcf -stand_call_conf...
View ArticleBug in HaplotypeCaller
Hi, I wanted to place what I believe is a bug report. Bug: If the haplotype caller assembles reads into identical haplotypes, then depending on arbitrary factors, it will emit different variant events...
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Bug in HaplotypeCaller: GT is called 0/1, but AD is 206,0
HI, I'd like to report a weird result from HaplotypeCaller. We have a patient sequenced by targeted sequencing on HNF1B. This patient has been confirmed to have a whole gene deletion of HNF1B so we...
View ArticleMemory error, and ProgressMeter strangeness during HaplotypeCaller
Log attached. It's become hard to tell what the columns mean in the ProgressMeter output, but I know this is strange. I see six columns in the output, but the header line has apparently nine columns...
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inconsistency between the read depth reported by HC and by samtools mpileup
Hi everyone, I'm calling SNPs by using GATK HC. I'm also using samtools mpileup to give specific base type and read depth information for each called SNP position (using the same bam file, of course)....
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(BPR2.0) Variant Discovery
This article is part of the workflow documentation describing the Best Practices for Variant Discovery in RNAseq data. See http://www.broadinstitute.org/gatk/guide/best-practices for the full workflow....
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(BP2.1) Calling Variants with HaplotypeCaller on RNAseq data
This article is part of the workflow documentation describing the Best Practices for Variant Discovery in RNAseq data. See http://www.broadinstitute.org/gatk/guide/best-practices for the full workflow....
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