Multithreading Queue with SGE
Hello, I'm trying to run GATK-Queue in my SGE environment to parallelize my pipeline, but I'm having trouble making use of multiple CPUs (-nct). I can run the test scala qscripts...
View ArticleProblem with allele specific annotation AS_QualByDepth (AS_QD) during variant...
Hi GATK team, First a big thank you for all your hard work in developing the tool and supporting the users! I am trying out the allelic specific(AS) annotations in version 3.6. While I have gotten a...
View ArticleGenotypeGVCFs error: does not inflate expected amount
Hi, I am running into a very confusing problem. I am running GenotypeGVCFs on ~30 gzipped and .tbi indexed vcf files. The program starts running ok, but then stops pretty quickly into the run with the...
View ArticleMESSAGE: Code exception (see stack trace for error itself) HaplotypeCaller
Hi, all: I meet some error while call variant with HaplotypeCaller, please help~~ Thanks a lot! my CMD: java -jar GenomeAnalysisTK-3.6.jar -T HaplotypeCaller -R...
View ArticleHaplotypeCaller missing a clear variant
Dear colleagues, I am comparing two callers and found some cases in which HC behaves strangely. Let's look into one of the cases. There's a site in which there are 15 bases overlapping. Of these, 6 are...
View ArticleHaplotype Caller excessive memory usage for a single sample in GVCF mode for...
I'm currently using the latest GATK stable version (3.6) with Java 8 to identify variants in RNAseq data for Sus scrofa samples. I'm having a lot of memory problems dealing with Haplotype Caller at...
View ArticleSex chromosome In VCF calling
Hi, I have made the calling using the HaplotypeCaller and then running the variant recalibration but I obtained 1/1 in some variants in chromosome Y and chromosome X for men and women. They are not...
View ArticleMESSAGE: Code exception (see stack trace for error itself)
Hi GATK Team, I am running HaplotypeCaller on my BAM file, command line: ... variants calling by gatk with multi sample is start ~... 2016-07-03 00:13:44: java -XX:ParallelGCThreads=5 -Xmx50g...
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 ArticleSingle sample vs Multiple samples Haplotype Caller
Salutations , Let me start by saying I'm pretty new in this whole bioinformatics thing. So probably I won't be adequate enough , please do bear in mind. I have the following questions. I have one...
View ArticleSubsetting contigs from existing .g.vcf's
Hi, I've used HaplotypeCaller to call variants on whole genome CRAMs without specifying regions. Now, I'd like to subset this data to chromosomes 1-22 + X without redoing the calling. Is there a...
View Articlebias towards the ref allele in Haplotypecaller
Hi, I've been calling SNPs of more than 10 DNAseq libraries in Arabidopsis and always get a strong bias in the number of calls for the reference allele (2-10 fold). I thought that HC might see errors...
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I expect to see a variant at a specific site, but it's not getting called
This can happen when you expect a call to be made based on the output of other variant calling tools, or based on examination of the data in a genome browser like IGV. There are several possibilities,...
View Articlequestion of Minimum frequency to call homozygote by HaplotypeCaller
Hi,I want to know the threshold to define homozygote and heterozygote .Other software set the frequency to call homozygote is 0.75. I can't find it in HaplotypeCaller document. Wish your reply.thanks.
View ArticleWeird Error When Calling Haplotype caller
So, I've experienced this weird runtime error everytime I call the HaplotypeCaller - the Error Message is "-88" and the stacktrace claims to have an ArrayIndexOutOfBounds error. I've built some of my...
View Articlecalling variants on haploid organism
Hi, I'm curious about something I find using HaplotypeCaller on my haploid fungus. (using it with -ploidy 1) In my vcf there are some variants with low variant allele frequency (around 50%). for...
View ArticleConflict between HaplotypeCaller variant and BAM
Hello, I'm using GATK version 3.6 to analyze a trio exome, and I followed the best practices (prinseq, bwa, markduplicates, baseRecal, printReads, HC and hard filtering, to resume the pipeline; with...
View ArticleCombine GVCF files problem
I used the following command to combine 3 VCF files which are outputs of HaplotypeCaller: java -jar data/GenomeAnalysisTK-3.2-2/GenomeAnalysisTK.jar \ -R data/ucsc.hg19.fasta \ -T CombineGVCFs \...
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(howto) Generate a "bamout file" showing how HaplotypeCaller has remapped...
1. Overview As you may know, HaplotypeCaller performs a local reassembly and realignment of the reads in the region surrounding potential variant sites (see the HaplotypeCaller method docs for more...
View ArticleStatus for dealing with paired-end reads
Hi all, new here and its my first post, so sorry if its not relevant enough. I have been thinking about the same problem that occurred here twice already, and i cannot seem to come to a conclusion on...
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