when to apply assembly-regon-padding step
Hi， I find that there are multiple steps in determining active regions in haplotypecaller, so I wonder when is assembly-region-padding is applied, is it applied during steps in determining active...
View ArticleHaplotypeCaller pooled sequence problem
Hi, I have a number of samples that consist of multiple individuals from the same population pooled together, and have been truing to use HaplotypeCaller to call the variants. I have set the (ploidy to...
View ArticleHow to run GATK directly on SRA files
Hello , I recently saw a webinar by NCBI "Advanced Workshop on SRA and dbGaP Data Analysis" (ftp://ftp.ncbi.nlm.nih.gov/pub/education/public_webinars/2016/03Mar23_Advanced_Workshop/). They mentioned...
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Haplotypecaller calls variants at a deletion region
Hi, I'm having a confusing problem when using haplotypecaller. Basically, I'm using haplotypecaller calling variants among more than 400 M. tuberculosis samples, sequenced with Hiseq2500 platform. I...
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VCF - Variant Call Format
This document describes "regular" VCF files produced for GERMLINE short variant (SNP and indel) calls (e.g. by HaplotypeCaller in "normal" mode and by GenotypeGVCFs). For information on the special...
View ArticleHow to best minimize variation between runs of HaplotypeCaller in GVCF mode?
I am using a combination of HaplotypeCaller local (non-spark), in GVCF mode, followed by GatherVcfs to merge them, and I get very different call results across runs. I would expect the...
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(How to) generate a complete realigned bam file using -bamout argument in...
Hello, I want to get a realigned bam file for other tools to call variants, so I used the -bamout argument in HaplotypeCaller. I found that bam file is incomplete when I used only -bamout argument....
View Articlefree of reference bias priors in HaplotypeCaller
Hello, I would like to replicate the behaviour of gakt described in Mallick et al. 2016 for the Simon's genomes data set. They explain in the supplementary information the following: "GATK...
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HaplotypeCaller: Alternate allele get called or not depending on -ip option
Hi, I'm currently analyzing some data (exome-seq) using HaplotypeCaller and get what seems to me an odd behaviour: The problem is that I've got a position which is clearly bi-allelic in IGV and that is...
View ArticleShould I provide the exome target list (-L argu) even while calling gVCF file...
Hi, Recently we performed exome sequencing using Nextera Illumina platform for three samples (Father, Mother and Son). I downloaded the exome interval list from Illumina's website. 1) Trimmed the raw...
View ArticleIs there a paper describing the »Haplotype Caller algorithm?
Hi, I'd like to ask you if there is a paper describing the Haplotype Caller algorithm, if you could please send me the reference. I have tried to find it, but I only found the paper on GATK which is...
View ArticleHaplotypeCaller sensitivity in large(ish) cohorts
One of my projects currently has ~150 patients (exomes) that I've been processing through the standard pipeline (2.8-1, including ReduceReads). In my most recent run through HC, I split the cohort in...
View ArticlePhantom indels from HaplotypeCaller?
Dear GATK users and developers, I am running HaplotypeCaller followed by ValidateVariants and the latter complains about variants that have called alternative allele without any observation for it....
View ArticleAllele Depth (AD) / Allele Balance (AB) Filtering in GATK 4
Hi, I am trying to filter my GATK 4.0.3 - HaplotypeCaller generated multi-sample VCF for allele depth (AD) annotation at sample genotype-level (so available in "FORMAT" fields of each sample). I think...
View ArticleSNP calling using pooled RNA-seq data
Hello, First of all, thank you for your detailed best practice pipeline for SNP calling from RNA-seq data. I have pooled RNA seq data which I need to call SNP from. Each library consists of a pooled...
View ArticleHaplotypeCaller on whole genome or chromosome by chromosome: different results
Hi, I'm working on targeted resequencing data and I'm doing a multi-sample variant calling with the HaplotypeCaller. First, I tried to call the variants in all the targeted regions by doing the calling...
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Haplotype caller not picking up variants for HiSeq Runs
Hello, We were sequencing all our data in HiSeq and now moved to nextseq. We have sequenced the same batch of samples on both the sequencers. Both are processed using the same pipeline/parameters. What...
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GATK HaplotypeCaller missing SNPs at the terminals of the segment when...
We are trying to call variants for Influenza A virus sequenced by MiSeq using HaplotypeCaller following GATK best practices (GATK version 3.7). However, when checking in IGV the called variants with...
View Articlei am running haplotypcaller in one bam file
java -jar GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T HaplotypeCaller -R reference/GRCh37/hs37d5.fa -I output.bam --dbsnp reference/gatkbundle/dbsnp_138.b37.vcf -o output.g.vcf -ERC GVCF i am trying...
View ArticlePhased Heterozygous SNP
Dear all, I have difficulties in understanding the genotypes of the phased SNPs. Here i have a SNP where only one read has a reference allele and 11 reads have an alternate allele and is called as...
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