HC step 3 : Evaluating the evidence for haplotypes and variant alleles
This document describes the procedure used by HaplotypeCaller to evaluate the evidence for variant alleles based on candidate haplotypes determined in the previous step for a given ActiveRegion. For...
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 ArticleUnusual False Positives from HC/UG on edges of small, very high-coverage regions
Hey there, I'm currently working on a project that uses the MiSeq system to perform very deep sequencing (5000x coverage) on a small set of genes related to a particular cancer type. I have had some...
View ArticleMissing QD tags at some positions
Hey there, How can it be possible that some of my snps or indels calls miss the QD tag? I'm doing the recommended workflow and I've tested if for both RNAseq (hard filters complains, that's how I saw...
View ArticleError when running HaplotypeCaller
Hi, I'm trying to call variants on WGS data using the following command (on a high-performance cluster using 4 cores per job) : java -Xmx6G -jar $CLASSPATH -T HaplotypeCaller --dbsnp GRCh37-lite.vcf...
View ArticleUnified genotyper and Haplotype Caller for exome sequencing data
Hello everyone, I have recently sequenced 15 sample exomes using the Ion proton system, which directly generates VCFs after sequencing runs. However, since I will be using GATK for downstream analysis,...
View ArticleGenotypeGVCFs "VCF is malformed" error message
Hi, I've tried my best to find the problem but without luck, so my first post... First the background: I have used HaplotypeCaller to make GVCFs per individual for 2 cohorts of 270 and 300 individuals...
View ArticleHaplotypeCaller INDEL calling, inconsistent with bamfile alignment
I have WES data of 235 samples, aligned using bwa aln. I followed GATK's Best Pratice for marking duplicates, realignment around INDEL, and BQSR until I got the recalibrated bamfiles. All these are...
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 ArticleMissing AC, AN, Af tagsin vcf files genrated with HaplotypeCaller/ GenotypeGVCFs
Following the the recommended best practice and using GATK v3.2, the raw vcf file created by haplotyecaller/GenotypeGVCFs does not contain any of AC, AN and AF tags. Is this an expected behaviour? This...
View Articlephased genotypes from HaplotypeCaller
Hi, Is there a way that HaplotypeCaller (or another tool) can output phased genotypes in the VCF file? Thanks! Andrew
View ArticleGATK HaplotypeCaller run
Hi, I am using HaplotypeCaller for variant calling on GATK version 3.2.2 on whole genome Illumina reads. I used the following command as per best practices with and without multithreading option...
View ArticleHaplotypeCaller shifts deletion CIGARs in -bamout
HI, I have noticed on the number of occasions that the cigar strings of deletions in the haplotype file generated with -bamout are incorrectly shifted by 1 or 2 basepairs. It does not affect variant...
View ArticleHaplotypeCaller error: Somehow the requested coordinate is not covered by the...
I am attempting to use the HaplotypeCaller to call indels and SNPs in genomes from the Illumina Platinum Genomes pedigree (http://www.illumina.com/platinumgenomes/). I did these steps before running...
View ArticleHaplotypeCaller error: Argument with name 'mbq' isn't defined
Hi, I ran HaplotypeCaller with the following command java -jar GenomeAnalysisTK-2.8-1-g932cd3a/GenomeAnalysisTK.jar -T HaplotypeCaller -minPruning 3 -R genome.fasta -I reduced.bam -o Chr10.vcf...
View ArticleHaplotypeCaller problems with ploidy argument
I am trying to use the HaplotypeCaller with a ploidy setting of 1 to genotype sex chromosomes in a single individual using the following command: java -Xmx4g -jar...
View ArticleQueue and PBS scheduler
I would like to run HaplotypeCaller on some WGS samples from 24 individuals. I have attempted to use the multithreading option but would instead like to use the scatter-gather approach with Queue on...
View ArticleRelease notes for GATK version 3.3
GATK 3.3 was released on October 23, 2014. Itemized changes are listed below. For more details, see the user-friendly version highlights. Note: at time of writing, the release process in underway. The...
View ArticleJoint calling of projects run on different exome-capture platforms
Hi, We have some exomes processed with GATK from one exome capture platform (Nimblegen SeqCap on HiSeq), and now I am going to analyze a small batch of exomes sequenced using a different platform...
View ArticleHaplotypeCaller on all dbSNP positions
Hi: I'm running HaplotypeCaller on whole-genome data. I'm interested in only several thousand specific positions across the genome, all of which are in dbSNP. Some of these are indels, which makes me...
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