what is defined as a candidate region in haplotypecaller?
I learn that HaplotypeCaller looks for candidate regions and builds a denovo assembly. So how is this region defined? How big is the region? Recently we found a six base pair insertion in an...
View ArticleShould I use UnifiedGenotyper or HaplotypeCaller to call variants on my data?
The HaplotypeCaller is a more recent and sophisticated tool than the UnifiedGenotyper. Its ability to call SNPs is equivalent to that of the UnifiedGenotyper, and its ability to call indels is far...
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 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 ArticleA real deletion x a false extended deletion?
Hello again, please, we need help understanding a deletion detected by HC. Here is the VCF line and the activeRegions output (attached): MT 9190 . CTGCACGACAACACAT C 1057.73 VQSRTrancheBOTH99.00to99.90...
View Article'Cannot trim a Haplotype without containing GenomeLoc'
Hi, I'm trying to call at known variant sites (human) in the Neanderthal (bam file), using HaplotypeCaller. I've altered the original vcfs...
View ArticleIndel Calling
I have Ion Torrent data. I am trying to call a variant that I know to exist (confirmed with Sanger). In the position where there is the known indel, I have a depth of roughly 80-90 (in two different...
View ArticleHaplotypeCaller and Coverage. I get ./. but I have coverage
Hi, I'm calling Variants with HaplotypeCaller in a population of 2 Parents and 7 F1-individuals. After read backed phasing I'm combining the vcf files of my genotypes with CombineVariants. In the...
View ArticleHaplotypeCaller and VariantRecalibrator with QUEUE
Hi team, I have a basic question, sorry. I am trying to use HaplotypeCaller and VariantRecalibrator with QUEUE but I don't know how add: VariantRecalibrator.mode = BOTH HaplotypeCaller.genotyping_mode...
View ArticleHaplotype caller Speed with Multi-sample variant calling
I am testing out GATK Haplotype caller to make it work with our existing variant calling pipeline. In our current pipeline which is based on GATK best practice, the variants are called globally across...
View ArticleGATK HaplotypeCaller isn't calling variants?
Hi guys, I am working with three genomes from the same species. I have managed to call variants between the reference and two of the genomes but the third seems to be having an issue that I don't know....
View ArticleEffect of using a ReduceReads bam or full bam on GATK 2.7 HaplotyeCaller+VQSR?
What is the expected effect of using GATK 2.7 HaplotyeCaller+VQSR on a WGS 30x bam or the same bam being processed through ReducedReads beforehand? Does one expect exactly the same variants called on...
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...
View ArticleHaplotypecaller, 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 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 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 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...
java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.haplotypecaller.LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(LikelihoodCalculationEngine.java:379) at...
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...
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