HC step 2: Local re-assembly and haplotype determination
This document details the procedure used by HaplotypeCaller to re-assemble read data and determine candidate haplotypes as a prelude to variant calling. For more context information on how this fits...
View ArticleHaplotypeCaller GVCF mode Qscript
I tried HaplotypeCaller on whole-genome sample in GVCF mode and it takes several days and ends up incomplete. I would like to use Queue script to parallelize the jobs. I am new to using Queue scripts...
View ArticleHaplotypeCaller/ Variantannotator no allele balance tag for all SNPs
Version 3.1.1. Human normal samples. I couldnt find AlleleBalance and AlleleBalanceBySample tags in my vcf outputs. Tags are not found even for single variant I tried HaplotypeCaller with -all or...
View ArticleInconsistent handling of high base quality scores
It seems as if the handling of sam/bam/cram files with higher-than-usual base quality scores is inconsistent. In particular, a base quality score of 93 causes HaplotypeCaller to throw an exception if a...
View ArticleHaplotypeCaller Re-Alignment Step
Hello community, I am really new to the field of genome analysis (I've got a computer science background). At the moment I am dealing with the topic of variant calling and decided to use / understand...
View ArticleNumber of Haplotypecaller output files
Hello! On certain runs I get only .vcf file as an output and sometimes I see both .vcf and .vcf.idx as output files. Is there an issue with the runs that yield only .vcf file and not .vcf.idx?
View ArticleRelease notes for GATK version 3.5
GATK 3.5 was released on November 25, 2015. Itemized changes are listed below. For more details, see the user-friendly version highlights. New tools MuTect2: somatic SNP and indel caller based on...
View Articleparameter questions for haplotypecaller
Hi GATK, I'm runing the GATK germline variant calling pipeline. I have some questions about realignertargetcreator and haplotypecaller's parameters. Please correct me at any point if I went wrong. For...
View Articlemany `LowQual` flags in output .vcf when using `HaplotypeCaller` with...
Hi GATK team, I am working on a pipeline for exome sequencing variant calling. And I am only interested in the genotype for some specific positions so I used GENOTYPE_GIVEN_ALLELES mode with given vcf...
View ArticleGeneration of haplotype or phase data for SNPs in the flanking region of STRs
Does anyone know of an effective way to determine haplotypes or phasing data for SNPs and STRs? I understand that STRs are inherently difficult for aligners; however, I'm trying to determine haplotypes...
View ArticleUsing HC GVCF mode for determining rate of heterozygosity
Hi GATK team, I was hoping I could get some insight on determining rate of heterozygosity from a gvcf file. We have three diploid lizard samples. Each was run through our GATK pipeline using HC in GVCF...
View ArticleVersion highlights for GATK version 3.5
The last GATK 3.x release of the year 2015 has arrived! The major feature in GATK 3.5 is the eagerly awaited MuTect2 (beta version), which brings somatic SNP and Indel calling to GATK. This is just the...
View ArticleDifference between vcf directly generated by HC and vcf generated from...
Hi, I have three general questions about using HaplotypeCaller (I know I could have tested by myself, but I figured it might be reliable to get some answer from people who are developing the tool): For...
View ArticleGenotypeGVCFs number of
Hi all, I'm very new to GATK. I'm trying to map an EMS mutation in Arabidopsis. I have fastq files of a wt M3 bulk and a mut M3 bullk (both offspring of the same parent). The strategy is to call for...
View Articleunified genotyper vs. haplotype caller w/ pedigree study, major discrepancies
Greetings. I've been exploring de novo mutation identification in the context of a pedigree of trios. I've run the UnfiedGenotyper (UG) given all the bam files for ~25 sets of trios and it appears to...
View ArticleHow the HaplotypeCaller's reference confidence model works
This document describes the reference confidence model applied by HaplotypeCaller to generate genomic VCFs (gVCFS), invoked by -ERC GVCF or -ERC BP_RESOLUTION (see the FAQ on gVCFs for format details)....
View Articlehelp diagnosing missed variants in amplicon data
Hi all, I'm relatively new to GATK. At first I was intimidated by the amount of documentation, but lately I've really come to appreciate how there are answers to nearly all questions somewhere on this...
View ArticleNo MQ annotation from Haplotype Caller in version 3.5 but does work in 3.4
I upgraded to GATK 3.5 to use MuTect2 and it works great! However, I'm now using the updated .jar in my germline variant calling pipeline and there's some issues. I only noticed it when I went to run...
View ArticleGATK Haplotypecaller missing variants
I am trying to use GATK HP ( v3.5 ) to call SNPs in amplicon seq data of a small genome of around 600bp. As shown in the attachment, the variants are not called between location 50 and 60, despite high...
View ArticleUnparsable vcf record with allele *
Hi guys, I have recently jointly called 27 full genome data using GenotypeGVCFs approach. While i was trying to extract some chromosomes from the final file, i got this error The provided VCF file is...
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