How do I turn off INDEL calling in HaplotypeCaller (i.e. only call SNPs)?
I know that for UnifiedGenotyper the option is -glm, but I don't see that available for HaplotypeCaller.
View Articlewhich DP value shuold I use ？
I used HaplotypeCaller module to detect mutations,I noticed that the DP values was different in the INFO column and in the FORMAT column ,like the picture: Why this happened ?which DP value shuold I...
View ArticleMultisample vs Single sample(Paired sample MUT &WT separate BAM files)
Hello, I'm currently working with zebrafish mutants, and compare phenotypically wild-type and mutant siblings for mutations. I have 3 different mutants, like 3 pairs of different Mutant and Wild type...
View ArticleWhy is HaplotypeCaller missing these two variants when they are homozygous?
I have some known variants called by a different caller, further confirmed by Sanger sequencing. I've noticed HaplotypeCaller (HC) will call variants at this location when they are in a heterozygous...
View ArticleMaximizing sensitivity of HaplotypeCaller for pooled sample
I'm attempting to call variants (primarily SNPs) with HaplotypeCaller from a pooled sample containing 95% wild-type and 5% polymorphic strain data (C. elegans, SE-50bp, 20-fold genomes). Per...
View ArticleHaplotypeCaller v3.7.0 alternative allele depth not emitted
Hi I just noticed the alternative allele read depth is missing for a true positive insertion called with HaplotypeCaller v3.7.0. #SNPs and Indels GVCF with Haplotypecaller...
View ArticleWhy analyze RNAseq samples together to boost the variant discovery ?
Hi, I'm working with RNAseq data from one patient (2 conditions), you recommend analyzing all samples together, because it will boost the discovery power, why ? Many thanx, Jennifer
View Article500 reads supporting reference allele, 0 reads supporting the alternate...
For one of my samples at one particular SNP, there appears to 500 reads supporting the reference allele and 0 reads supporting the alternate allele. However, GATK still did not call a genotype:...
View ArticleHaplotypeCaller generates diff results on different CPUs
I encountered an interesting problem: running HaplotypeCaller on different machines generates different result for 2 sites. The machines use the same input BAM file, same reference, same java...
View ArticleWDL Repository?
Hello, Is there a central repository where one can look at pre-existing WDLs to see if they meet a need? For context, I'm trying to find some WDLs that may implement some splitting/merging of fastq...
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...
View ArticleGenotypeGVCFs on pooled data sets fail for ploidy > 10
Hi, I'm currently analysing a data set of six pools, 25 individuals in each (ploidy 50), of a non-model organism. I initially ran HaplotypeCaller with parameter -ERC GVCF and then attempted to do joint...
View ArticleDifferent results of haplotypecaller using Base Quality Recalibration Score
Dear GATK team, I have analyzed samples sequenced with an Illumina custom amplicon sequencing kit. I aligned samples with BWA mem algorithm and then I applied haplotypecaller following the suggestions...
View ArticleGATK best pratices for RNA-seq somatic mutation finding
Dear All, I have followed GATK best practices for finding Somatic mutations from cancer versus normal sample from RNA-seq data using Mutect2 as the final caller and rest all quality control steps as...
View ArticleBamout file shows a consistent deletion that is not reported in VCF
Dear GATK team I ran HaplotypeCaller on a bam file, which is the alignment of a single bacteria sample to its reference genome. To understand the calling process I wanted to compare the resulting VCF...
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Variant calling inconsistencies using GVCF
Before starting, I'm a grad student without formal training in bioinformatics so I've mainly learned from online forums. That being said, if this question is stupid or I'm missing critical information,...
View ArticleBest Practices for Batch Calling Malaria
Since there is no gold standard SNP database for Plasmodium vivax, my lab and I have been tinkering with a pipeline for variant calling with GATK. I'm pretty confident with the basic framework we have,...
View ArticleAre my data and research question appropriate for analysis with HaplotypeCaller?
Hello GATK team! I'm having a hard time finding discussion of and examples of use of HaplotypeCaller by researchers with similar data and research questions as me so apologies for posting on your forum...
View ArticleHaplotypeCaller raises an error with -A BaseCountsBySample
Hi GATK team , FYI I'm getting the following error with GATK 3.7: java -X -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R human_g1k_v37.fasta --validation_strictness LENIENT -I .bam.list \ -o...
View ArticleHaplotypeCaller can't find variants when using GENOTYPE_GIVEN_ALLELES?
Hello, I want to call variants in some samples with the HaplotypeCaller using the GENOTYPE_GIVEN_ALLELES mode. I have used a vcf file with 2 variants for the -alleles option, and a bed file with...
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