Downsampling with HaplotypeCaller
Hello, I'm running the Haplotype Caller on 80 bams, multithreaded (-nt 14), with either vcfs or bed files as the intervals file. I am trying to downsample to approximately 200 reads (-dcov 200)....
View ArticleGATK3.3 HaplotypeCaller reassembly made the variant calling differently
Hi, The variant was called by MiSeq reporter and GATK2.7 UnifiedGenotyper with VAF 19% after soft-clipping the primer sequences, as also seen in BAM file got according to GATK best practice (BWA, indel...
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Best Practice pipeline for WES, including VQSR - what is best?
I am currently processing ~100 exomes and following the Best Practice recommendations for Pre-processing and Variant Discovery. However, there are a couple of gaps in the documentation, as far as I can...
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 ArticleWhy is HaplotypeCaller not calling obvious SNPs by default but requires...
Hi, I'm calling SNPs for bacterial genomes. I've been using UnifiedGenotyper to call SNPs, and I'm looking to migrate to HaplotypeCaller. This change from UnifiedGenotyper to HaplotypeCaller requires...
View ArticleHaplotypeCaller variant with 0/0 genotype
Hi, There are some confused result found in the output gvcf of HaplotypeCaller. Why the genotypes is 0/0 but called a GC->G deletion? see below for example. chr8 118915071 . GC G,<NON_REF> 0 ....
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Best practice for Panel Sequencing
Dear all, we use the Broad best practice pipeline to call germline variants on Panel-seq data, i.e. our chip comprises the Omimom. Hence, it is not a small target set but significantly smaller than for...
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Distribution of GQ called by HaplotypeCaller GenomeAnalysisTK-3.2-2
Hi GATK team, I have recently performed an analysis to try and select a GQ cut-off to be applied to WES data post-VQSR (applied 99.9% to the data). The WES data was called using HaplotypeCaller...
View ArticleHaplotype Caller: how to determine java memory requirements?
Hi, I am interested in calling SNPs for a set of 150 bacterial genomes (genome size ~1Mb). I'm attempting to use the HaplotypeCaller and am running into errors with the java memory: There was a failure...
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CombineVariants unwanted merge behaviour at identical positions
Question: Is it possible to have CV merge like bcftools does it? I get this warning, when running UG in GGA mode using an -alleles vcf generated with CV: WARN 10:17:21,394 GenotypingGivenAllelesUtils -...
View ArticleHaplotypeCaller report different genotype on the same location with different...
Hi GATK team, I am using the GATK 3.3 HaplotypeCaller. I found if i use different -L i will have different genotype on the same location. My para is very simple: -T HaplotypeCaller -R ucsc.hg19.fasta...
View ArticleHaplotypeCaller - Genotype Given Allele Mode
Hi Team, I want to call variants for some samples using Genotype Given Allele mode(GGA) of HaplotypeCaller. I have used UnifiedGenotyper earlier in GGA mode. I am not sure about the right approach to...
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You 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,...
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(howto) Generate a "bamout file" showing how HaplotypeCaller has remapped...
1. Overview As you may know, HaplotypeCaller performs a local reassembly and realignment of the reads in the region surrounding potential variant sites (see the HaplotypeCaller method docs for more...
View ArticleCoverage bias in HaplotypeCaller
Hi, I am doing joint variant calling for Illumina paired end data of 150 monkeys. Coverage varies from 3-30 X with most individuals having around 4X coverage. I was doing all the variant detection and...
View ArticleCan (or will) Queue use PBS Professional job dependencies?
Question Hey folks, We've run in to a situation where we have hundreds of queue managed GATK HaplotypeCaller.scala jobs which we'd like to run. This has led to hundreds of instances of Queue.jar in...
View ArticleGenotypeGVCFs sees DP incorrectly in INFO, not FORMAT field
I have a potential bug running GATK GenotypeGVCFs. It complains that there is a DP in the INFO field, but in my haplotypecaller-generated -mg.g.vcf.gz's I do not have a DP in the info, I do have DP in...
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(BP2.1) Calling Variants with HaplotypeCaller in gVCF mode
This article is part of the workflow documentation describing the Best Practices for Variant Discovery in DNAseq data. See http://www.broadinstitute.org/gatk/guide/best-practices for the full workflow....
View Articlevariant detection: DP and Mendelization
Hi, Two questions, which relate to Unified Genotyper or Haplocaller: Detecting and determining the exact genotype of an individual seems to be inaccurate at read depths less than 10X. This is because...
View ArticleHaplotype Caller and overlapping Paired end reads
Hi there, I've been looking at some WES data where I am comparing pre and post GT refinement workflow data and came across where it seems like to me that HC does not take into account overlapping...
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