Recommended protocol for bootstrapping HaplotypeCaller and BaseRecalibrator...
I am identifying new sequence variants/genotypes from RNA-Seq data. The species I am working with is not well studied, and there are no available datasets of reliable SNP and INDEL variants. For...
View ArticleHow to get exact allele frequency using HaplotypeCaller-GATK4 and speed up...
Hi there, I have performed HaplotypeCaller in GATK4 (version:4.0.9.0) for variant calling of germline DNA. Here are the results in the vcf file. chr1 17365 rs369606208 C G 146.77 ....
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Variant not being called by HC GATK v3.7-0-gcfedb67
Hello, We are calling variants on data that has been sequenced on NextSeq platform. We have been using the same pipeline , with the same commands since a year and in all our runs we have a control...
View ArticleActiveRegion determination (HaplotypeCaller & Mutect2)
This document details 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 ArticleMeaning of --min_base_quality_score
What is the --min_base_quality_score mean ? Is it base on the mapping quality in the sam/bam file or the sequencing base quality? I'm a little bit confused by the description of the tool document in...
View ArticleHaplotypeCaller says dict does not exist, but it does!
Hi All, I am running HaplotypeCaller and getting the error: ERROR MESSAGE: Fasta dict file...
View ArticleHaplotyperCaller optional arguments:
Hello GATK, I'm using GATK 4.0.6 HaplotypeCaller to call wild bird SNP and InDel sites. Command nohup java -jar /opt/GATK-4.0.6/GATK-4.0.6-local.jar HaplotypeCaller -R bird_genome_reference.fa -I...
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HaplotypeCaller reassembles reads so that no variants are called in a...
Hi. gatk-4.0.7.0 java openjdk version "1.8.0_181" I've encountered a problem while running HaplotypeCaller in -ERC BP_RESOLUTION --genotyping-mode DISCOVERY --output-mode EMIT_ALL_CONFIDENT_SITES mode...
View ArticleGetting out-of-memory errors while running the worflow for germline short...
I'm trying to run the wdl posted on the gatk-workflows Github page, under the gatk4-germline-snps-indels repository. The wdl is "haplotypecaller-gvcf-gatk4.wdl" I'm attempting to run this wdl locally...
View ArticleClarification of parameters for HaplotypeCaller
Hi I'm new to GATK and am looking into using HaplotypeCaller to call chloroplast variants in a plant. I am interested in both the variant sites and invariant sites in my sample (relative to my...
View ArticleExamples of exome fastq and vcfs using GATK4 HaplotypeCaller + bwa mem 0.7.17?
Hi all, I'm working on a GATK 4.0 fastq to vcf pipeline, and I'm wondering for validation purposes if anyone knows where I could find, or could share with me, exome fastq files and their corresponding...
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 ArticleMNP and HaplotypeCaller GVCF mode
Hello I am attempting to run HaplotypeCaller in a way that will merge adjacent SNPs into MNPs. To do so I set --max-mnp-distance to 1 or 2. This worked well when I did not used GVCF mode. However, when...
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HC overview: How the HaplotypeCaller works
This document describes the methods involved in variant calling as performed by the HaplotypeCaller. Please note that we are still working on producing supporting figures to help explain the sometimes...
View Articlejava.lang.NullPointerException in HaplotypeCaller when generating gVCF with...
I am running the latest gatk 4.0.11.0 on aligned reads from whole exome sequencing from TCGA to generate gVCF files. After generating the gVCF file, gatk is crashing with a null pointer exception. I...
View ArticleVariant discovery starting from gVCF file
Hello, as the title suggests I'm looking to use the variant discovery tools, specifically SNP discovery. However I am not starting with a FASTA or BAM file, indeed I do not currently have access to...
View ArticleUsing HaplotypeCaller 3.5 vs HaplotypeCaller 4.0 joint calling large cohorts
We've been testing published Broad "production" workflow for paired-end single sample alignment and variant calling github.com/gatk-workflows/gatk4-germline-snps-indels ("paired-end single sample...
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I got a question about the kmer length you parsed during the second step of...
As I screenshot, I found HC respectively parse the sequence corresponding to the ActiveRegion on reference genome and reads to kmers in length of 10 and 25. Furthermore,...
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Inconsistent results with HaplotypeCaller on haploid organism
Hello GATK team, I would appreciate some help in understanding how GATK works in GVCF mode on my data. Here is my data example I'm usign GATK v3.8: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 328-16...
View ArticleHC step 4: Assigning per-sample genotypes
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...
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