VQSR filtering and dbSNP
Hi, For VQSR filtering, it's assumed that all calls made by HaplotypeCaller or MuTect2 are put into VQSR? Polymorphic sites should only be culled AFTER the vcf is annotated with VQSLOD scores, and a...
View ArticleHow can I force HaplotypeCaller to call a genotype -- want to avoid gt=./.
In a single sample vcf I have homozygous snp that is not assigned a genotype, the genotype is missing (gt=./.). What knobs can I turn on HaplotypeCaller (in GATK 3.8 or 4.1.2) to assign a genotype to...
View ArticleBeginner's question: Why can't I start the analysis run on Terra?
Hello. I am new in genomic analysis and GATK. I am trying to start Haplotypecaller workflow on Terra. I have uploaded aligned genomic reads (bam file and bam index) and used appropriate genome assembly...
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Does GATK HaplotypeCaller has resume analysis feature
Hello there, I am calling variants on 800 exome samples using Haplotypercaller for some reasons the caller stopped the analysis on certain location on chromosome 5 (after 5 weeks and i have 10 weeks to...
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Variant Caller and BAM file INFO not matching
Hello, I am using gatk-4.0.3.0 following the Best practices. BWA-> Picard Mark Dup -> GATK Base Recalib/Apply -> HC variant calling per sample For one of our samples, we have a variant called...
View ArticleGVCF of amplicon sequencing
Hi, I'm trying to generate a GVCF with HaplotypeCaller based on amplicon (PCR) sequencing, and bases towards the end of the reads (~10 bases last bases) consistently get genotype quality of 0, even...
View ArticleGATK v4.0.1.1 HaplotypeCaller
I am using GATK v4.0.1.1 HaplotypeCaller for variant analysis. (paired-end DNA sequenced data mapped to the reference using BWA mem). The command I used; “gatk HaplotypeCaller –R Reference.fna –I...
View ArticleGatk haplotype caller java error
Hello GATK team, I am trying to run gatk haplotypecaller (version 4.1.1.0) on a bam file and used the following command: "java -jar /ufrc/gatk-4.1.1.0/gatk-package-4.1.1.0-local.jar -T HaplotypeCaller...
View ArticleShould I use GATK haplotype caller/unified genotyper for finding SNPs in 2...
I have two whole genome sequenced bacterial samples. I have their contigs file with me. I would like to pairwise comparison between isolate1 and isolate2 to identify SNPs between them. Should I use...
View ArticleAll ALT fields are the same after GenomicsDBImport and GenotypeGVCFs
Hi GATK team, I'm running GATK 4.1.3.0 to perform targeted single-cell genotyping, where each sample in the output VCF is a single cell (10-20k samples total per VCF). I've noticed something strange in...
View ArticleEmitting variants with low mapping quality
Hello, I am validating a new exome sequencing analysis pipeline using in-house-generated data from sample NA12878 and the Genome in a Bottle high confidence calls for this sample. I am using GATK...
View ArticleHaplotypeCaller generate incorrect heterozygous Calls
Hi, We have used GATK 3.6 and GATK 4.1 haplotype caller, to generate the variants, unfortunately, we are getting lots of incorrect heterozygous calls. Even only one read supports the variant it is...
View ArticleHow to get a smaller list of deNovo SNPs between 3 genotype
Hello. I am currently working on maize whole genome dataset and I have 3 samples- WT, MT and B73. I obtained the VCF files for all 3 datasets using the haplotype caller. However, the list of SNPs that...
View ArticleGATK Exception in HaplotypeCaller
Hi, I am using gatk 4.0.8.1 HaplotypeCaller for making g.vcf. I am running follwing command gatk --java-options "-Xms24g -Xmx48g" HaplotypeCaller -R new_hg38.fa -I S11_.sorted.BQRC.bam -O S11.g.vcf -L...
View ArticleWhat exactly is DP and how filtered is it?
I have read somewhat contradictory things across the documentation as to what DP actually measures, and I can't quite tell if I'm missing some distinction between the "different" DPs. I have read that...
View ArticleHow can a homozygous reference 0/0 genotype (GT) have a heterozygous phased...
Dear GATK support team, Multi-sample variant calling files made with GATK4 have both genotype, genotype phase and genotype phase block information....
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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 ArticleDiscovering singletons with GenotypeGVCFs?
Hi, I have several samples that I ran HaplotypeCaller (in normal mode) with that I am looking to discover germline variants from. I read that GenotypeGVCFs isn't good with discovering singletons, and...
View Articlenon-reference allele didn't be called into vcf by HC
Hi GATK team I ran HC joint calling and found out that some non-reference alleles didn't appear in the vcf. Most of these allele seems to reside on the region of relatively poor alignments. My first...
View ArticleHow does MAPQ affect haplotypecaller during germline calling
I understand that, during germline calling, pairHMM calculates the likelihood of each haplotype by taking base quality into consideration. My question is: what role does MAPQ play during germline...
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