HaplotypeCaller on whole genome or chromosome by chromosome: different results
Hi, I'm working on targeted resequencing data and I'm doing a multi-sample variant calling with the HaplotypeCaller. First, I tried to call the variants in all the targeted regions by doing the calling...
View ArticleSeveral Annotations not working in GATK Haplotype Caller
I am using Genotype Given Allele with Haplotype Caller I am trying to explicitely request all annotations that the documentation says are compatible with the Haplotype caller (and that make sense for a...
View ArticleClik here to view.
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...
View ArticleGATK3.8 vs GATK4 HaplotypeCaller
Hello, maybe I'm asking a naive question and maybe it has been answered somewhere else, but as the title states are there differences in the algorithm of the HaplotypeCaller between GATK3.8 release and...
View ArticleWARN messages with Haplotype Caller
Hi, I began a run using the --emitRefConfidence GVCF command asking for a .g.vcf file to be output for a single sample. Which is running (yay)! So far, it is still running and has thrown up several...
View ArticleMemory error when using scatter-gather (haplotypecaller + GenotypeGVCFs) on...
Dear GATK team, I have prepared 100 WES processed BAMs and try to call variants and output them in a single VCF. I used scatter-gather WDL scripts following...
View ArticleHC Tag
Hello, I'm looking at the HC tag that comes out of the --bamOutput option in HaplotypeCaller in the corresponding bam file that is produced. I've noticed that some real reads (i.e. ones not labeled as...
View ArticleHow to best minimize variation between runs of HaplotypeCaller in GVCF mode?
I am using a combination of HaplotypeCaller local (non-spark), in GVCF mode, followed by GatherVcfs to merge them, and I get very different call results across runs. I would expect the...
View ArticleIn which step exactly the allele depth / frequency is used during variant...
I was thinking of how allele depth / frequency affect variant calling. I know that the HC is using Bayes to call variant. The question is how is allele depth / frequency information used during the...
View ArticleHaplotype Caller ERC BP Res with nonref bases explicitly detailed
Hi GATK Team! I was wondering if there is a way to get Haplotype Caller in ERC BP Resolution mode to emit details for every base for every position? That is, for each position rather than just emitting...
View ArticleDoes GenotypeGVCFs call SNPs fixed in only 1 sample?
Apologies if this was addressed elsewhere, but I have looked carefully through the documentation. Simply put: using the joint analysis pipeline of GATK's HaplotypeCaller (-ERC GVCF) ->...
View ArticleHaplotypeCaller haploid GVCF format error?
Hi all, I prepared a clean Bam file following GATK Best Practice and used GATK4 HaplotypeCaller to create a gvcf with ploidy1 option: gatk-4.0.2.1/gatk HaplotypeCaller --native-pair-hmm-threads 24 -I...
View ArticleHaplotypeCaller crash with long allele in --alleles VCF
I am running HaplotypeCaller with the --alleles option and it is crashing. I've traced it to a very long line in the --alleles VCF file, with a very long allele. The line is: chr4 1394536 ....
View ArticleGenotypeGVCFs Estimated Runtime 5.9 YEARS!!!
Hello, I have 3 de novo transcriptomes for which I am trying to genotype all SNPs. Originally, I asked a question about whether the joint genotyping pipeline will correctly identify SNPs fixed in one...
View ArticleHaplotypeCaller crash expected haplotypes.size() >= eventsAtThisLoc.size() + 1
I'm running HaplotypeCaller (GATK 4) with --alleles argument and it is crashing on a particular --alleles VCF file record with a stack trace with error "expected haplotypes.size() >=...
View ArticleHow to run GATK directly on SRA files
Hello , I recently saw a webinar by NCBI "Advanced Workshop on SRA and dbGaP Data Analysis" (ftp://ftp.ncbi.nlm.nih.gov/pub/education/public_webinars/2016/03Mar23_Advanced_Workshop/). They mentioned...
View Articlewhen to apply assembly-regon-padding step
Hi， I find that there are multiple steps in determining active regions in haplotypecaller, so I wonder when is assembly-region-padding is applied, is it applied during steps in determining active...
View ArticleHaplotypeCaller pooled sequence problem
Hi, I have a number of samples that consist of multiple individuals from the same population pooled together, and have been truing to use HaplotypeCaller to call the variants. I have set the (ploidy to...
View ArticleDoes Haplotypecaller assign genotype for each allele separately?
Hi, I read how haplotypecaller assign genotype in the following link, it says that for each position haplotypecaller will calculate the best genotype, so I wonder, if the positions are close, then will...
View Articlefree of reference bias priors in HaplotypeCaller
Hello, I would like to replicate the behaviour of gakt described in Mallick et al. 2016 for the Simon's genomes data set. They explain in the supplementary information the following: "GATK...
View Article