Haplotypecaller, change setting after the run!
--stand_emit_conf and --stand_call_conf is by default set to 30 Everything lower will be "LOWQUAL", but is it possible to set --stand_emit_conf and --stand_call_conf set to 2, without running...
View ArticleEffect of cohort in HaplotypeCaller
I'm trying to measure the effect of the composition of a cohort on the calling of individual sample. So my cohort includes 46 Caucasian and 1 Japanese (J1) exome seq samples from 1KG. I want to check...
View ArticleHaplotypeCaller gave different results if include --dbsnp argument
Hi, I used following commands to call variants from exactly the same file by HaplotypeCaller. However, I got different results. The results from case1 are not consistent to case2. In some chromosomes,...
View ArticleHaplotypeCaller and Allele balance issue
Hi Team! I have an issue that I'm not sure how to solve. I'm using HaplotypeCaller with a three member family and I have some calls when the HOM/HET call doesn't match with what we expected: chr1...
View ArticleHaplotypeCaller...
java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.haplotypecaller.LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(LikelihoodCalculationEngine.java:379) at...
View ArticleHaplotypeCaller Incorrectly making Heterozygous Calls (Again)
Hi For GATK: GenomeAnalysisTK-2.4-7-g5e89f01 It would appear that the issue with the HaplotypeCaller making incorrect Het calls when it should be Hom has turned up again (if it ever actually went...
View ArticleHow does GATK determine GT when calling variants?
Looking closely at our vcf file produced by HaplotypeCaller we noticed disagreement between PL values and GT in some variants. For example. 1 762589 rs71507461 G C 21714.69 PASS [clipped]...
View ArticlePairHMM Log Probability cannot be greater than 0 Error with HaplotypeCaller
Dear All, I've encountered the following error while processing one of the regions from an interval file that I want to re-discover/genotype with the HC. Note that I've processed the other 4.2mln...
View ArticleHaplotypeCaller scattered job run time
Hi, I just managed to use HaplotypeCaller with the lasted version of Queue to call variants on 40 human exomes. The HaplotypeCaller job were scattered into 50 sub jobs and spread in our cluster with...
View ArticleUsing the reference confidence calculation mode and generating a GVCF [RETIRED]
This document is out of date and has been replaced by the following: http://www.broadinstitute.org/gatk/guide/article?id=4017 As of GATK 2.7, the HaplotypeCaller is now capable of emitting a per-bp or...
View ArticleStrange genotype calling with HaplotypeCaller
I cannot understand some of HC's calls. It is rare, but occasionally HC will call individuals as 0/1 when their ADs are 0,50+ (clearly 1/1). I tried looking at the output bams at those positions, but...
View Articleproblem with reference genome in variant calling
Hi, I’m trying to use GATK for variant calling. I have had some problems preparing the hg19 reference genome. I haven’t done the alignment myself, but gotten the .bam files already done. I how ever...
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 ArticleHaplotypeCaller Multisample Variant Calling
Hey there! I've been using HaplotypeCaller as part of a new whole genome variant calling pipeline I'm working on and I had a question about the number of samples to use. From my tests, it seems like...
View ArticleDownsampling with HaplotypeCaller
Hello, I'm running the Haplotype Caller on 80 bams, multithreaded (-nt 14), with either vcfs or bed files as the intervals file. I am trying to downsample to approximately 200 reads (-dcov 200)....
View ArticleBug in various tools, 2.4-7 : "ArrayIndexOutOfBoundsException"
As reported here: http://gatkforums.broadinstitute.org/discussion/2342/unifiedgenotyper-causes-arrayindexoutofboundsexception-3-how-to-fix-it...
View ArticleHaplotypeCaller on haploid genomes
I'm trying to run HaplotypeCaller on a haploid organism. Is this possible? What argument should I use for this? My first attempt produced a diploid calls. Sorry for the silly question
View ArticleHaplotypeCaller Error: Mismatch between the reference haplotype and reference...
Hi I have been running HaplotypeCaller on >700 monkey alignments and came across this error in some intervals: ##### ERROR...
View ArticleShould I use UnifiedGenotyper or HaplotypeCaller to call variants on my data?
Use HaplotypeCaller! The HaplotypeCaller is a more recent and sophisticated tool than the UnifiedGenotyper. Its ability to call SNPs is equivalent to that of the UnifiedGenotyper, its ability to call...
View ArticleHaplotypeCaller DP reports low values
Dear GATK Team, I've recently been exploring HaplotypeCaller and noticed that, for my data, it is reporting ~10x lower DP and AD values in comparison to reads visible in the igv browser and reported by...
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