DP field Mutect2
Hi all! I have used Mutect2 in order to do variant calling. I have obtained my vcf file but I don't have DP field in records section of the file, it is reported only in the header section. I can see...
View ArticleNot to generate final svdiscovery.dels.vcf
Hi All, I was running java -Xmx16g -cp ${classpath} \ org.broadinstitute.gatk.queue.QCommandLine \ -S ${SV_DIR}/qscript/SVDiscovery.q \ -S ${SV_DIR}/qscript/SVQScript.q \ -cp ${classpath} \ -gatk...
View Articlecan ValidateSamFile check on CRAM files?
I'm trying to validate a set of cram files, however, I'm getting the error shown below. I'm not sure if it is because I'm using a CRAM file, I have problems with the htsjdk library or the cram files...
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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How long does it take, Part 2
A while back, I posted this article about work done by the Intel Bio Team to benchmark the speed and resource utilization of each step in the per-sample segment of the germline variation pipeline...
View ArticleMuTect2 Output -- How can this be somatic mutation
n_lod t_lod_fstar t_lod_fstar__INFO__ n_genotype n_ref_count n_alt_count 50.33 PASS 16.43 0/0 448 149 n_allelic_depth n_QSS n_alt_allele_seen i_n_REF_F1R2 i_n_REF_F2R1 448,149 14273 False 214 234...
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Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode
This document describes the new approach to joint variant discovery that is available in GATK versions 3.0 and above. For a more detailed discussion of why it's better to perform joint discovery, see...
View ArticleError "Mate unmapped flag should not be set for unpaired reads" after RevertSam
Hi, I am following the Tutorial#6484, Reverting a bam file into ubam, which runs successfully. However, when I tried to apply MarkIlluminaAdapters, I got an error message of "Mate unmapped flag should...
View Articleerror when merge discovery output
Dear GenomeSTRiP developer, I've run the svdiscovery script and it hangs on after all individual SV detection finished. The error message I've got is the following: INFO 23:14:42,482 HelpFormatter -...
View Articleabout running variant calling ( final UnifiedGenotyper and HaplotypeCaller...
Hello, I am currently having a hard time looking for a fatal error that considerably reduces the file size of the vcf files using UnifiedGenotyper and HaplotypeCaller process. (there is a huge...
View Articlev3.7-0-gcfedb67: -T RealignerTargetCreator does not support --known blah.vcf.gz
Hi, it seems GATK does not relaize that it has opened a vcf.gz (actually vcf.bgz file). java -Djavaio.tmpdir=. -jar /scratch/mmokrejs/GATK/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T...
View ArticleWhat is the size of the internal window used by gatk haplotypecaller's...
Hello gatk community, Since gatk haplotypecaller is ran by a sliding window approach, the variant calling on each position seems to also depend on the presence/type/absence of variants on the flanking...
View ArticleError details: The contig order in variant and reference is not the same...
Hi GATK team I am trying to compare variants called with GATK 3.7 and samtools mpileup. I have used the same reference genome files, same bam files. Right now, I just wanted to pit everything in the...
View ArticleHow to obtain a GATK commercial license?
I've sent an email to "softwarelicensing@broadinstitute.org", but have not heard back. Is there some other way that I can get some information on the licensing and costs?
View ArticleHaplotype Caller Error: Graph must have ref source and sink vertices
I have been following the GATK Best Practices document 'Best Practices for Germline SNP & Indel Discovery in Whole Genome and Exome Sequence' (though without the base recalibration step as I lack a...
View ArticleMergeBamAlignment Fails, can use AddOrReplaceReadGroups to debug?
Hello, I've been running a drop-seq experiment, and the 2nd to last command fails: java -Xmx4000m -jar 3rdParty/picard/picard.jar MergeBamAlignment REFERENCE_SEQUENCE=mm10/mm10.fasta...
View ArticleFormat of gatk4cnv_padded_target_bed_capture in "GATK 4 CNV Proportional...
Hi, I am trying to run "GATK_Somatic_CNV_Toolchain_Capture" and absolute on targeted sequences with no matched normal. I understand that the first step is to run "GATK 4 CNV Proportional Coverage for...
View ArticleOutput active regions in GATK4 HaplotypeCaller
Hi What would be the best way to output active regions from GATK4 HaplotypeCaller? In GATK 3.x, an option --activeRegionOut <file name> could be used to write active regions in a TSV file....
View ArticleVariantFiltration error
I am trying to filter variants in the file "variants.vcf" that was produced by the GenotypeGVCFs. It keeps running in an error that I don't know how to fix. I used this command to run...
View ArticleVariant recalibration (WQSR) after pooled calling
Hi - we have whole genome samples consisting of non-barcoded DNA from 50 diploid individuals with 80-120x coverage. We use version 3.5-0-g36282e). We align, then use BQSR. For variant calling, we...
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