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I expect to see a variant at a specific site, but it's not getting called
This can happen when you expect a call to be made based on the output of other variant calling tools, or based on examination of the data in a genome browser like IGV. There are several possibilities,...
View ArticleCan GenotypeGVCFs be ran without filtering?
For bacteria genomes I use the "Best Practices" and the HaplotypeCaller to call variants. I would like to output a VCF containing all positions I can then parse on my own. I'm using -ERC BP_RESOLUTION...
View ArticleCalculateGenotypePosteriors - skip non-diploid sites?
This is more of a feature request than anything else. I'm implementing the genotype refinement best practices guidelines for some trio WGS data sets. The probands are mostly male, and chrY causes...
View ArticleBatch effects begone: Introducing the Functional Equivalence data processing...
By Eric Banks, Director, Data Sciences Platform and original member of the GATK development team Ever since the GATK started getting noticed by the research community (mainly as a result of our...
View ArticleData Model Magic?
Hi All, Stuck again. The first step in my pipeline is to convert fastq -> unaligned BAM, which was successful. This is done so that there are several read groups (corresponding to different...
View ArticleData Model Magic
Sorry for repost, was for some reason in "Zoo and Garden!! Hi All, Stuck again. The first step in my pipeline is to convert fastq -> unaligned BAM, which was successful. This is done so that there...
View ArticleIntervals and interval lists
Interval lists define subsets of genomic regions, sometimes even just individual positions in the genome. You can provide GATK tools with intervals or lists of intervals when you want to restrict them...
View ArticleMeaning of error: expected haplotypes.size() >= eventsAtThisLoc.size() + 1
Hi, I am running HaplotypeCaller (GATK 4.0.0.0) in genoype-given-alleles mode using a VCF of common coding germline variants. Please see the error below. Can anyone help to point me in the right...
View ArticleVariantFiltration and BaseRecalibrator
So I've created a pipeline to make a known.snp.vcf for my species without known snps for BaseRecalibrator: For a subset of my samples (~5% of my dataset, 10 samples): I ran HaplotypeCaller on each bam...
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Off-label workflow to simply call differences in two samples
Given my years as a biochemist, if given two samples to compare, my first impulse is to want to know what are the functional differences, i.e. differences in proteins expressed between the two...
View ArticleUnexpected result for VQSR with non-model organism (Plasmodium falciparum -...
Hi, I am variant calling wgs (~best practices; group calling for g.vcf) in Plasmodium falciparum and I would like to filter the call data using VariantRecalibrator VQSR, as opposed to setting hard...
View ArticleStructuralVariationDiscoveryPipelineSpark Erro: CouldNotReadImageException
I am running the following script with GATK 4.0.0.1.1. gatk --java-options "-Djava.io.tmpdir=tmp" StructuralVariationDiscoveryPipelineSpark \ -R $REF \ --aligner-index-image...
View ArticleHow is a haplotype called by HaplotypeCaller across the genome with RADseq data?
Hi, I had a question about how is a haplotype called by HaplotypeCaller across the genome with reduced representation sequencing data. I have ddRADseq data from a diploid organism and I used...
View ArticleTesting Intel Arria® 10 GX FPGA implementation of HaplotypeCaller (PairHMM)
Hi, I am a researcher from Chinese of Academy of Sciences. I am trying to test the FPGA implementation of the HaplotypeCaller (PairHMM) on GATK 3.8-0-ge9d806836, using a Intel Arria® 10 GX FPGA (Arria...
View ArticleHow to include non variant sites in the output vcf of GenotypeGVCFs?
Hello I'd like to include confident non variant sites in my downstream analyses. If I understand correctly, this was possible in previous versions with --includeNonVariantSites but I'm not seeing an...
View Article[ERROR] Malformed VCF: empty alleles are not permitted in VCF records
I am running BaseRecalibrator for my RNA-seq: java -jar -Xmx120g ${GATK} -T BaseRecalibrator -R "${reference}" -I "${file4}" -knownSites "${gerVar}" -knownSites "${somVar}" -o...
View Article"Could not open array genomicsdb_array at workspace" from GenotypeGVCFs in...
I experience Issues with GenotypeGVCFs and GenomicsDB input in the final GATK4 release using the official Docker image. This does not occur using the 4.beta.6 release. It looks like there has been a...
View ArticleCombineGVCFs java.lang.IllegalArgumentException: Unexpected base in allele...
Hi, Hoping to work around the limitations of GenomicsDBImport I've used CombineGVCFs to combine my data into batches of 200 and then combined them again into a master GVCFs for genotyping....
View Articlethe order of merge and mark duplicate
I have a whole genome sequencing sample. That consist of 1fastq file per lane. That consist of multiple file per sample that produced per lane. After I merge multiple bams, I progress MarkDuplicates...
View ArticleSVPreprocess Mismatch found between genome mask and reference
Hello. I'm trying to execute the SVPreprocess step on 48 samples I have. I've gotten the program to run but two of the SVPreprocesss*.out files contain errors/run failures. In one: SVPreprocess-5.out...
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