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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...

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Several 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...

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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...

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GATK3.8 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...

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WARN 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...

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Memory 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...

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HC 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...

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How 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...

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In 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...

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Haplotype 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...

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Does 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) ->...

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HaplotypeCaller 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...

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HaplotypeCaller 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 ....

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GenotypeGVCFs 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...

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HaplotypeCaller 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() >=...

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How 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...

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when 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...

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HaplotypeCaller 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...

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Does 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...

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free 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...

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