Why mutations have much less read depth after variant calling by...
hi, I'm new here. I am trying to find germline mutations in a mutiplex_pcr generated NGS data with Haplotypecaller (GATK 4.0.4.0 ). I am confused about that why mutations have much less read depth...
View Articledefault read filter in haplotypecaller
Hi, Where can I find which read filters that are applied by default in Haplotypecaller in GATK4? (GATK web page or github page)
View Articlehaplotypecaller gvcf very slow on draft WGS
Dear GATK people, I am trying to call SNPs out of 150 samples of WGS data on a non-model species (coral). The reference is a draft genome of 500 MB, each sample has roughly 15 M paired end reads....
View ArticleOmission of IndelRealignment in production pipelines using GATK 3.5
It was announced with the release of GATK 3.6 that it is no longer necessary to run IndelRealigner when HaplotypeCaller will be used to call variants. We are testing the published "prod" single-sample...
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What is a GVCF and how is it different from a 'regular' VCF?
Overview GVCF stands for Genomic VCF. A GVCF is a kind of VCF, so the basic format specification is the same as for a regular VCF (see the spec documentation here), but a Genomic VCF contains extra...
View ArticleWhat is the difference between the data fed to the 1st and 3rd steps of the...
Hello everyone, Can anyone please explain to me whether we need all the reads for the 3rd step of the HaplotypeCaller ("Determine likelihoods of the haplotypes given the read data") as evidence or only...
View ArticleEvaluating the evidence for haplotypes and variant alleles (HaplotypeCaller &...
This document details the procedure used by HaplotypeCaller to evaluate the evidence for variant alleles based on candidate haplotypes determined in the previous step for a given ActiveRegion. For more...
View ArticleVariant calling on BAMS from different Alignment Tools
I have a question about performing variant calling on multiple BAM files that have been generated using 2 different alignment tools (for example - 'BWA-mem' and 'Novoalign' in my case). For example -...
View ArticleAlternate Alleles in VCF are more than 1 base
Hi there, I've removed INDELS from a multi-sample vcf from HaplotypeCaller using SelectVariants. However, the ALT 'SNPs' are more than a single nucleotide substitution. Eg....
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HaplotypeCaller in a nutshell
This document outlines the basic operation of the HaplotypeCaller run in its default mode on a single sample, and does not cover the additional processing and calculations done when it is run in "GVCF...
View ArticleMissing annotations in the output callset VCF
The problem You specified -A <some annotation> in a command line invoking one of the annotation-capable tools (HaplotypeCaller, MuTect2, GenotypeGVCFs and VariantAnnotator), but that annotation...
View ArticleHaplotypeCaller producing output without any vcf
Hello, I am using GATK 4.0.8.1in Ubuntu 18.04 LTS and javac -version => javac 1.8.0_181. I am basically trying to call variants from Targetted DNA sequencing data using HaplotypeCaller. Though...
View ArticleIs GATK4 HaplotypeCaller in evaluation phase?
Hi GATK team, Congratulations on the release! I just found this public method in FireCloud that notes that HaplotypeCaller in GATK4 should not be used for production use yet since it is still in...
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ALT * no deletion
Hi： my vcf, there is a "*", but I can't find the deletion in OF2-M bam by IGV 。I can't understand why ? GATK is 3.7 version。Haplotyper --emit_mode gvcf + GVCFtyper genome is not human. Thank you！ CHROM...
View ArticleAssigning per-sample genotypes (HaplotypeCaller)
This document describes the procedure used by HaplotypeCaller to assign genotypes to individual samples based on the allele likelihoods calculated in the previous step. For more context information on...
View ArticleWhy does HaplotypeCaller (HC) use a flat prior in joint calling?
In genotyping, P(G|D)=P(G)P(D|G)/P(D). Why HC uses a flat P(G) instead of computing one based on cohort allele frequencies?
View ArticleIs it possible to suppress the NON_REF tag on variant calls?
Hello, In GVCF output from HaplotypeCaller, each line contains the allele, including the lines with explicit variant calls. Is there a simple way to suppress the allele on variant calls? Also, what is...
View ArticleMissing chr in gVCF
Hi, I have generated a gVCF file using GATK-3.7 and it is completed without any error. However, i notice only few chromosome names in the first column of the gVCF file: java -Xmx10G...
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Why is there difference of variants between after-BQSR bam and...
Dear GATK team, Hi, I have followed Best Practices to find out germline variants (GATK-3.7) of my samples designed by case-control study for ~500 samples in total. I have run BQSR, Prind Reads, and...
View ArticleInference of genotype likelihoods for lower ploidy based on genotyping at...
Let's say I have a bunch of mixed ploidy individuals (with biallelic markers) in my data. Some are tetraploid and some are diploid. But I choose to run GATK HaplotypeCaller (to get genotype...
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