HaplotypeCaller
A new tool has been released!Check out the documentation at HaplotypeCaller.
View ArticleHaplotype caller
Hi, The version of GATK i have installed is unable to find command "HaplotypeCaller", i have the following versions of GATK installed. version 2.0-0-gb142977 (built from git) version 2.0-0-g4c0ffd4...
View ArticleHaplotypeCaller and Reduced BAMs
Hi, I would like to ask if the most recent version of GATK is stable enough for HaplotypeCaller to work well with Reduced BAMs. If not, can you give an estimate of when would that be in place? Thanks...
View ArticleRelease notes for GATK version 2.1
Base Quality Score Recalibration Multi-threaded support in the BaseRecalibrator tool has been temporarily suspended for performance reasons; we hope to have this fixed for the next release. Implemented...
View ArticleError in Haplotype Caller
Hi, I am trying to run the latest version (GenomeAnalysisTK-2.0-35-g2d70733) of the HaplotypeCaller on some .bam files that I had prepared according to the Best Practice v.3. Now GATK reports the...
View ArticleDoes HaplotypeCaller cost a lot of RAM?
I tried to run several HaplotypeCaller jobs simultaneously on a node. But sometimes, not all the time, they caused the nodes collapse. I noticed that HaplotypeCaller sometimes occupied tens of GB of...
View Articlehaplotypecaller indel format
Hi there, I've done with a run of HaplotypeCaller on my samples. I'm now analysing everything with snpEff, although I'm doing this "outside" GATK. I had to stop the analysis because a huge number of...
View ArticleHaplotypeCaller with Queue
Is there any example of a queue script calling variants with the HaplotypeCaller? thanks! Francesco
View ArticleHaplotypeCaller --fullHaplotype not outputting full haplotype
I am also having a problem with HaplotypeCaller - when I set the flag to print out full haplotypes, no haplotype files are created. Here is my command: java -jar...
View ArticleHaplotypeCaller - single block subsitution or multiple SNVs?
Hello GATK team, I notice that HaplotypeCaller will sometimes call a single block substitution variant where UnifiedGenotyper would call two separate SNVs, e.g.: HC chr12 93147901 . CGTGCCA TGTGCCT...
View ArticleExpected file size - Haplotype Caller
Hi All, I've been attempting to use the haplotype caller on my 50x coverage exome data. The bam being parsed is about 12G. Each time, the caller runs for many hours and then the output is only the...
View ArticleHaplotypeScore not annotated?
Hi there, I'm running into an issue with my Queue pipeline, with variants called with HaplotypeCaller. Once I get the raw VCF file, I use VariantAnnotator before VQSR: however, no HaplotypeScore...
View ArticleVariant Recalibration - Number of Whole Exome Samples Needed and Where?
Hello, I've just made a long needed update to the most recent version of GATK. I had been toying with the variant quality score recalibrator before but now that I have a great deal more exomes at my...
View ArticleRelease notes for GATK version 2.2
GATK release 2.2 was released on October 31, 2012. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history Base Quality...
View ArticleEMIT_ALL_CONFIDENT_SITES for bacteria
Hello, I am running the variant caller to identify SNPs and Reference Calls in a bacterial genome, which means I am running with -ploidy 1, -glm POOLSNP and -prnm POOL as suggested in other regions of...
View ArticleHaplotypeCaller rs annotation
Hi there, I'm running now the new GATK 2.2-2 version and I noticed an issue with HaplotypeCaller I had in the previous version I was using. Despite adding the dbSNP ROD to the walker, the emitted VCF...
View Articlehaplotypecaller doesn't emit genotype at all sites
I've tried to get genotype for all sites provided in interval file using haplotypeCaller. If using unifiedGenotyper, I can get the result by setting "output_mode EMIT_ALL_SITES". But haplotypeCaller...
View ArticleWhy did HaplotypeCaller report HET genotype for loci without reads supporting...
Hi GATK team, When I checked closely by IGV, I found many of the loci, with all reads supporting variants, were reported as a HET genotype by HC. After go back to the VCF result, I still don't...
View ArticleSome abnormal outputs of HaplotypeCaller
Hi GATK team, I found some abnormal output lines in VCF file which was generated by HaplotypeCaller in GATK 2.2.5 pipeline, with default parameters: 0/2 genotype reported for a bi-allelic loci: SCF35...
View ArticleIs this expected that HaplotypCaller identified 40% more variants by 2.2.5...
Hi GATK team, I recently downloaded GATK2.2.5 and re-analyzed a small part of my data which was analyzed by2.1.8 pipeline previously, following the same parameters. However I found the new pipeline...
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