Default value of HaplotypeCaller
Hello Everyone, I am working with gatk tool package "HaplotypeCaller" to find SNPs and Indels. I want to know what are the initial default values of HaplotypeCaller, and can I change these values...
View ArticleGATK 3.7 HaplotypeCaller
Hi, I've been looking at the release notes for GATK 3.7. I would like to know if turning on the -newQual setting for HaplotypeCaller would be considered Best Practice for WGS and WES pipelines. Thanks,...
View ArticleHC step 3 : Evaluating the evidence for haplotypes and variant alleles
This document describes 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...
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 ArticleI have 50 exome samples belong to 25 families. Do I run GenotypeVCFs on...
We have exome sequenced data for 50 samples in total for a cardiac disease. But they have been sequenced in different batches. Even some of the batches were 2 years old. We have relationship...
View ArticleThree allele calls for a diploid organism
Hello Everyone, Not sure what to make of this one-- I have a diploid fish that I'm examining an interesting variant for. I generated a "bamout" file using Haplotype caller for one particular individual...
View Articlerules for max_alternate_alleles in HaplotypeCaller
Hi, I can't come to any clear conclusion how this parameter works. Help me, please. I worked on the same files with exact command but the max_alternate_alleles. In first command I put 1 for its...
View ArticleRead-Backed phasing and Indels
Hi, I'm calling Haplotypes of a diploid genome with the HaplotypeCaller and using the Read-Backed Phasing tool afterwards. I believe that Indels can't be phased so far. My output files look like the...
View Articlemissed variant calling for amplicon-based sequencing data using HaplotypeCaller
Hi all, I am using GATK v3.7 HaplotypeCaller to genotype 2000 dbSNP variants, including SNPs and INDELs, from amplicon-based sequencing data. --alleles is applied in HC, however, nearly 100 SNPs can...
View ArticleHow to run HaplotypeCaller in pooled DNA data locally using scatter-gatter...
Hola WDL team, I have whole-genome data of pooled DNA per population (one BAM file for each population) of several populations, and have access to a local Desktop with 125 GB RAM, 32 cores. My goal is...
View ArticleConflict between HaplotypeCaller variant and BAM
Hello, I'm using GATK version 3.6 to analyze a trio exome, and I followed the best practices (prinseq, bwa, markduplicates, baseRecal, printReads, HC and hard filtering, to resume the pipeline; with...
View ArticleUnexpected genotypes in GenotypeGVCF output
Hello GATK Team, I have 21 bam files that I ran through HaplotypeCaller in GVCF mode followed by GenotypeGVCF, using Version=3.4-0-g7e26428. I found a few entries that I am having a difficult time...
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HaplotypeCaller and detection of large indels
Hi, I am wondering about the detection of large indels with the haplotypecaller. I have an example where to my mind there is quite clearly a large deletion (a couple of kb) in the sample, but it is not...
View ArticleMissing gentoypes despite high number of reads
Dear GATK-team GenotypeGVCFs, sets all genotypes as missing for a large part of a gene I am interested in, even though there seem to be lots of reads in all individuals for those sites. I have the same...
View Articlewhat is max-alternate-alleles ?
HI, firstly ,set max-alternate-alleles is 6 . I guess max-alternate-alleles means that at a site , the ref allele is A , the number of other alleles type (C,G) found by reads do not more than 6 . but...
View ArticleGATK HaplotypeCaller produces no output
Hi, A colleague was experiencing a very long run-time for a GATK HaplotypeCaller run and asked me to look at it. I noticed that although it had been running for about 5 days, it hadn't even created a...
View ArticleHC step 1: Defining ActiveRegions by measuring data entropy
This document describes the procedure used by HaplotypeCaller to define ActiveRegions on which to operate as a prelude to variant calling. For more context information on how this fits into the overall...
View ArticleIssue with reassembly (potentially) in HaplotypeCaller
I have a question about how the reassembly works in HaplotypeCaller from GATK version 3.6-0-g89b7209. I have been checking the SNPs called in IGV and I have found a couple of regions that very clearly...
View ArticleAC,AF, and AN INFO fields are not defined in output from HaplotypeCaller
Hi, I have a problem where the output vcf from the haplotypecaller doesn't include meta-information lines for the AC,AF, and AN info fields, yet one of the records in the vcf contains these info...
View ArticleCall Varients from RNA-seq for RNA editing detection
Dear GATK staff I would like to use the GATK tool for the detection of possible RNA editing events. I followed the RNA-seq best practice up to the variant calling step itself. There I hesitate to use...
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