VQSR background GVCFs for new exome library
Hello GATK team, Hope you are all doing good. We have been performing VQSR on our exome samples fine until now, but now we are in a bit of a bind. All of our exome samples up to this point belong to...
View Articlememory requirements for MUTECT2/GATK
Dear all, please could you advise if there is any way to reduce the memory requirements for GATK/MUTECT2 (in GATK versions 3.5-3.8) ? Recently, we've started running MUTECT2 per chromosome on a SGE...
View ArticleGATK 4 GenotypeGVCFs tool does not accept multiple GVCF files?
Hi, I have migrated from GATK 3.7 to GATK 4 tools for my whole genome and whole exome pipelines. I am using the alignment data for a family trio (aligned by BWA-MEM). Following the best practices, I...
View ArticleGenotypeGVCFs tool gives different output depending on the order of input GVCFs?
Hi, I have been using GATK GenotypeGVCFs tool (versions 3.5, 3.7 and 4.0). It has come to my attention that depending on the order of input GVCFs, the output slightly changes, i.e. the total number of...
View ArticleHow does HaplotypeCaller discriminate between heterozygous and homozygous...
Dear members of the GATK team I am using different GATK modules to detect some SNPs in my RNASeq data set. I did a test run for one individual to get an idea about the output of HaplotypeCaller. I know...
View ArticleGATK4 beta2 GenotypeGVCFs produces VCF with no records, just a header
Hi, GATK4 beta2 GenotypeGVCFs produces a VCF with no records on my test data. The file does contain a valid VCF header. The commands that I used for GenomicsDBImport and GenotypeGVCFs are below. Both...
View ArticleHow to make results from GAT4.beta.3 "HaplotypeCaller" comparable to...
We have been using “UnifiedGenotyper” of GATK2.7 for SNV calling, with "EMIT_ALL_SITES" mode, which always generate great results. We recently learnt GATK4 is in-development, with UnifiedGenotyper...
View ArticleWhen should I use -L to pass in a list of intervals?
The -L argument (short for --intervals) enables you to restrict your analysis to specific intervals instead of running over the whole genome. Using this argument can have important consequences for...
View ArticlenewQual argument
Hi, I was wondering if -newQual the default behavior in GATK 3.8 HaplotypeCaller? I receive an error that the argument is not available when I try to run HaplotypeCaller with GATK 3.8. Thank you! Mariam
View ArticleThe error of the genomestrip's Svpreprocess
Hi,I'm just use the genomestrip to call the sv from pigs. I have 30 bams and then follow the introduction to prepare the reference file ,genomeMaskFile ,copyNumberMaskFile and ploidyMapFile files.But...
View ArticleDepthOfCoverage in v4
https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php I would like to create sample_interval_summary files for use...
View ArticleFiltering Mutect2 somatic calls with PoN dataset
Hello, I have build my PoN data and would like to filter out artifacts and germ-line variants by inspecting a panel of normal samples and rejecting candidates that are present >= 2 normal samples....
View Articlejava.lang.RuntimeException: Error processing input from file.bam: Invalid...
I'm getting the error above when I run Genome Strip discovery pipeline. I would appreciate help troubleshooting. Below are the lines in the output beginning with the first error through the end of the...
View ArticleFastaAlternateReferenceMaker output contig names?
Is there any way to make the output from FastaAlternateReferenceMaker not rename the contigs? I'm running a pipeline that (theoretically) has worked with previous verions of GATK (...
View Article(howto) Apply hard filters to a call set
Objective Apply hard filters to a variant callset that is too small for VQSR or for which truth/training sets are not available. Caveat This document is intended to illustrate how to compose and run...
View ArticleRecommendations on using different versions of GATK for variant calling and...
Dear GATK Team, From what I understand, best practices recommend using the same version of GATK for variant calling (with HaplotypeCaller) and joint genotyping (with GenotypeGVCFs). Let's say, we found...
View ArticleHow to set ploidy option for haploid joint variant calling?
Hi, I have 1500 bacterial clean and sorted alignment bam file and I want to call variant and produce a multisample vcf file including 1500 sample. Bacteria are haploid. Do I need to set ploidy option...
View ArticleGenotypeGVCF on pooled data running out of memory despite providing 512GB to...
Dear GATK staff, I am doing SNP calling with GATK 3.8 on whole genome sequences of 12 pools (50 diploid individuals in each pool, genome size ~900 Mbp) of a non-model organism with scaffolded reference...
View ArticleCan I use htsjdk Java plugin to return a byte range of a requested chromosome...
I've read through this documentation: https://samtools.github.io/hts-specs/SAMv1.pdf From my very rough understanding, the index file requests information from the .bam file by using requesting the...
View ArticleDepth threshold for Mutect2
What is the default threshold of depth to call somatic mutations in Mutect2? Thank you.
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