Any way to call INDELS worth 150p -200 bp long using HaplotypeCaller
Hello, I used UnifiedGenotyper and HaplotypeCaller on my sample to get out INDELS and SNPS. There is a 147bp deletion in one of the genes(working with yeast genome)(see attached file). But this...
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 ArticlegVCFs for Targeted Resequenced data
Hi For targeted re-sequenced data, can we do variant calling using HaplotypeCaller in gVCF mode followed by using GenotypeGVCFs for joint genotyping ? Would the following best practices work for...
View ArticleEffect of Queue scatter+gather on HaplotypeCaller?
Gidday, I have a question about choosing the number of scatter jobs when running the HaplotypeCaller in Queue. Basically, is there a hard and fast rule about how small you can split up the job? From...
View ArticleHaplotypeCaller crash with multithreading + SSE
I recently ran the HaplotypeCaller using both the new --pairHMM options and -nct 2, and I encountered a crash in the program (8 of 96 runs crashed). I have rerun the analysis without the "-nct 2"...
View ArticleObtaining the "AB" information from HaplotypeCaller and GVCFs
Using GATK 3.1-1, I seem to be unable to get the "AB" (AlleleBalance) annotation for the calls using the HaplotypeCaller -> GenotypeGVCFs pipeline, and I'm not sure how to get it. Our current...
View ArticleGATK-Queue: script fails to call multiple processors
Hello, I adapted the example UnifiedGenotyper script to run HaplotypeCaller. Unfortunately, so far I haven't been able to get it to use multiple CPUs. I am using a server with 64 cores (AMD Opteron)...
View ArticleHow to select specific chromosomes and convert chromosome notation in BAM for...
I am preparing BAM files from the 1000 genomes project to use in my GATK pipeline (along with other already processed BAMs) and I have the following issues: chromosome notation on my BAMs is from...
View ArticleHaplotypeCaller java.lang.NullPointerException Error
Hi, I'm still new to bioinformatics so I'll apologise in advance if I've made an obvious error anywhere here... I am running HaplotypeCaller on four species of rodent (Mus musculus and three wild,...
View Article--stand_emit_conf and --stand_call_conf setting in Haplotypecaller
I have processed samples using GATK 3.1 Haplotypecaller according to the RNA Seq best practice. Haplotypecaller is set with --stand_emit_conf = 20 and --stand_call_conf = 20 options, but I could find...
View ArticleHaplotypeCaller stopping midway without error, probably ram related
I'm running the HaplotypeCaller on a series of samples using a while loop in a bash script and for some samples the HaplotypeCaller is stopping part way through the file. My command was: java -Xmx18g...
View ArticleHaplotypeCaller seems not working well for several of my samples
Hi, I am using the GATK v3.1-1-g07a4bf8. It seems to me that HaplotypeCaller made quite a lot more heterozygous calls for several of my samples. As you can see from the scatter plot, for those...
View Article0/0 genotypes in GenotypeGVCFs
Hi, I want to call both confident variants and confident homREF genotypes using gatk 3.x style (pretty much like EMIT_ALL_CONFIDENT_SITES in UnifiedGenotyper). I first use HaplotypeCaller with -ERC...
View ArticleMerging Genome VCF's for the Same individual
Hi this is pretty much a feature request for something I think would be useful, I mentioned it briefly at the Brussels workshop and it seems like it might be possible. In a couple of projects I'm...
View ArticleOdd distribution of Coverage for GATK HaplotypeCaller Variants
Hi we've been looking at results of a recent run of GATK-HC (3.1-1) using the new N1 pipeline and we've been seeing something odd in the distribution of the Depth of Coverage (Using DP from the...
View Articlemerging bam files for an individual
I'm running HaplotypeCaller in GVCF mode, followed by GenotypeGVCF. For some individuals, I have more than one aligned bam file. Do I need to combine the individual's bam files in HaplotypeCaller to...
View ArticleMissing positions in the GVCF file
Hello, It seems the banded gvcf produced by HaplotypeCaller is missing many positions in the genome. We are not able to find half the specific positions we want to look at. To be clear, these positions...
View ArticleHow to get the number of forward/reverse reads in the final VCF output?
I don't see any information from this post http://gatkforums.broadinstitute.org/discussion/1268/how-should-i-interpret-vcf-files-produced-by-the-gatk, I was wondering if it's possible to get the number...
View ArticleRecall variants with haplotypeCaller
Hi, We work with around 600 human samples right now. We run haplotypeCaller on a group of 100 samples at a time (using GATK 2.7.2). But when this is done some groups have variants that is not found in...
View ArticleRelease notes for GATK version 3.2
GATK 3.2 was released on July 14, 2014. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history We also want to take this...
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