IndexOutOfBoundsException in HaplotypeCaller (GATK 3.2)
Hi, I get an error when using HaplotypeCaller (GATK version 3.2 and latest nightly build) on a specific BAM File: java.lang.IndexOutOfBoundsException: Index: 28, Size: 6 at...
View ArticleI have a error message that Index 25, size 8.
Hi I tried to call variant (HaplotypeCaller) after finishing Recalibrate(PrintReads) command. below is my command java -Xmx512m -Djava.io.tmpdir=./tmp/ -jar ../GenomeAnalysisTK.jar -T HaplotypeCaller...
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 ArticleHaplotypeCaller 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 ArticleHandling Multimappers
Hi, I am wondering how HaplotypeCaller in GATK 3.1 handles multimappers? I thought I read that they are passed over for variant calling but stay in the realigned, recalibrated BAM for 'completions...
View ArticleHaplotypeCaller genotype likelihoods
I have been reviewing some of my call data from a recent large exome run and after reviewing heterozygous calls made by HaplotypeCaller, I decided to confirm the base change in my recalibrated bam...
View ArticleI do not seem to be able to run the HaplotypeCaller with the...
I am using the HaplotypeCaller with GATK version 3.2-2. While it runs with the default EMIT_VARIANTS_ONLY option, it crashes when I try using the EMIT_ALL_CONFIDENT_SITES option. The stack trace is...
View ArticleSNPs Call using HaplotypeCaller
I am using the following script to call-variants from RNAseq data using HaplotypeCaller. However, in the VCF output I only have 0/1 and 1/1 genotype and there is no 0/0 genotype. How I can get all 3...
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 Articlethe Filter field in gvcf file created by HaplotypeCaller
Hello, I ran HaplotypeCaller on few projects. In the output gvcf file, the "Filter" field is always "." From the gvcf header, I understand that Filter can also be "LowQual". from the documentation, I...
View ArticleMissing variant while useing HaplotypeCaller
We are analysing monozygotic twins while using the HaplotypeCaller but we see some weird things. Not all SNPs are seen by the HaplotypeCaller while the bam file as input has clearly the SNP in there,...
View ArticleCan I retrieve the haplotypes assembled from HaplotypeCaller?
I am using HaplotypeCaller with a sample which I expect to be entirely homozygous. Therefore I only really expect 1 haplotype per site and others may be reads derived from paralogs/repeats not present...
View ArticleNaming SNPs..
Can a GATK tool automatically name detected variants, i.e. assign them a unique identifier within user-specified parameters?
View ArticleHaplotypeCaller does not output reference haplotype in bamout
Hi, I am using HC in GATK v3.2-2-gec30cee and trying to visualize the locally reassembled reads in IGV. For one sample, which is hetRA, the bam file produced by -bamout shows the reads and the variant...
View ArticleAny ploidy goes!
Until now, HaplotypeCaller was only capable of calling variants in diploid organisms due to some assumptions made in the underlying algorithms. I'm happy to announce that we now have a generalized...
View Articleparallel runs in genotypegvcfs ?
Hi, I am running HaplotypeCaller -ERC GVCF for a cohort in parallel per sample per chromosome and combined the data using CombineGVCFs across the cohort on per chromosome basis. Can I run the...
View ArticleStrange results generated from HaplotypeCaller when comparing "-minPruning 3"...
Hi GATK developer, I am working on a human WES project with an average sequencing depth 42X per individual. Recent version of GATK (v3.2-2) was used in my study. To investigate which "-minPruning"...
View ArticleRod span is not contained within the data shard...
Hi, We ran HaplotypeCaller on some bams and got the same error on them: Rod span is not contained within the data shard, meaning we wouldn't get all of the data we need. Here is my command: java...
View ArticleGATK 3.2-2 bug: ConcurrentModificationException
Hi, I encountered a ConcurrentModificationException on several bam files using HaplotypeCaller 3.2-2 that ran just fine on 3.1 using the same number of threads. Here is the stack trace:...
View ArticleGATK 3.2-2 bug: NullPointerException
Hi, I encountered a NullPointerException in 3.2-2 using the HaplotypeCaller on a BAM that run just fine on 3.1. Here is the stack trace: java.lang.NullPointerException at...
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