HaplotypeCaller speed
Hi, how does the speed of the haplotypeCaller usually compare to that of the UnifiedGenotyper? When I try to use it, it seems to be about 90x slower. these are the command lines I use: java -jar...
View ArticleEMIT_ALL_SITES in HaplotypeCaller
If I run HaplotypeCaller with a VCF file as the intervals file, -stand_emit_conf 0, and -out_mode EMIT_ALL_SITES, should I get back an output VCF with all the sites from the input VCF, whether or not...
View ArticleDownsampling Experiment
Hello! Trying to downsample in an orderly fashion in the name of experimentation, and in doing so would like to specify just one chromosome for the experiment - so I picked chromosome 17 with -L and a...
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 ArticleFILTER column in vcf file from HaplotypeCaller
I used a cohort in running HaplotypeCaller. Some of values in the FILTER column of the resulting vcf file are ".", what does that mean? Here is one example (not all columns included): #CHROM POS ID REF...
View Article(howto) Call variants with HaplotypeCaller
Objective Call variants on a single genome with the HaplotypeCaller, producing a raw (unfiltered) VCF. Caveat This is meant only for single-sample analysis. To analyze multiple samples, see the Best...
View ArticleCore dump with HaplotypeCaller using GATK 3.7
I'm trying to run HaplotypeCaller on a single RNAseq BAM file, but I keep getting a core dump. I've tried allocating more memory (up to 150 GB RAM) and reverting to single-thread mode, but...
View ArticleForgot to add -ERC GVCF when using haplotypecaller
Hi, I have used the haplotypecaller to call the variants for my each sample without -ERC GVCF. Thus, I can not use the GenotypeGVCFs to merge them together. What should I do to resolve this problem?...
View ArticleHaplotypeCaller Reference Confidence Model (GVCF mode)
This document describes the reference confidence model applied by HaplotypeCaller to generate a per-sample GVCF, invoked by -ERC GVCF or -ERC BP_RESOLUTION. As explained here, HaplotypeCaller works by...
View ArticleIs it useful to call LeftAlignIndels after IndelRealigner
Hi, In my pipeline to find variants in bacterial genome, I am first calling IndelRealigner and then calling variants using HaplotypeCaller. As left aligning of indels seems to be an important step,...
View ArticleCan HaplotypeCaller be used on drug treated samples?
Hello, I am working on a RNASeq data which consists of liver samples from donors. It is a case-control study where 12 samples are divided as Normal (control) and Rifampin Treated (case). I want to...
View ArticleHaplotypeCaller and reads mapped to multiple locations
Dear GATK team, I've been trying to use GATK to call SNPs from RNA-Seq data mapped to a transcriptome assembly. I used Bowtie2 for the read mapping. I apologize if the information is already posted,...
View ArticleIs GATK4 HaplotypeCaller in evaluation phase?
Hi GATK team, Congratulations on the release! I just found this public method in FireCloud that notes that HaplotypeCaller in GATK4 should not be used for production use yet since it is still in...
View ArticleOpenMP multi-threaded AVX-accelerated native PairHMM in HaplotypeCaller not...
I'm unable to get a multithreaded instance of PairHMM to work in HaplotypeCaller with JDK 1.8 on my local machine (Intel 4770K 8-core i7 processor) running MacOS 10.12.6. I've tried both a pre-built...
View ArticleWGS+WES combined discovery/genotyping
Hi GATK team, Hope you had great holidays! We're analyzing small families where some individual have been sequenced by WES (HiSeqX) and others by WES (HiSeq4000). Could you please advise on the best...
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Missing or Inconsistent call between single-sample and multi-sample SNP calling
Dear all, I have generated a gVCF file using HaplotypeCaller (v3.7)and searched for a specific variant of interest which looks like below: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT N417 chr1 627033...
View ArticleRecommended 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...
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Seeing multiple calls for the same position
Hello, I am running a trio through the best practices pipeline for 3.7 and finding an unexpected result. I am seeing some positions that are being called multiple times with different calls. First, as...
View ArticleMeaning of error: expected haplotypes.size() >= eventsAtThisLoc.size() + 1
Hi, I am running HaplotypeCaller (GATK 4.0.0.0) in genoype-given-alleles mode using a VCF of common coding germline variants. Please see the error below. Can anyone help to point me in the right...
View ArticleTesting Intel Arria® 10 GX FPGA implementation of HaplotypeCaller (PairHMM)
Hi, I am a researcher from Chinese of Academy of Sciences. I am trying to test the FPGA implementation of the HaplotypeCaller (PairHMM) on GATK 3.8-0-ge9d806836, using a Intel Arria® 10 GX FPGA (Arria...
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