i_variant_quality_by_depth/i_genotype_quality interpretation
When interpreting the output of HaplotypeCaller, what do the i_variant_quality_by_depth and i_genotype_quality columns represent and which of these would be a good value on which to base an assessment...
View Articlea question about running HaplotypeCaller with intervals
Hi, I have a question when running HaplotypeCaller functions with intervals on exome-seq data. Here is the command I used: java -jar gatk-package-4.0.6.0-local.jar HaplotypeCaller -R...
View Articlecan VariantsToTable output the raw genotype call (i.e., 0/1) rather than the...
I'm interested in getting simple "heterozygous" or "homozygous" designations for all of the samples/SNPs in my multisample VCF file. In the past, I have been using the -GF GT option in VariantsToTable,...
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Haptyepecaller calls incorrect genotype in several site
Hi, I found that the Haptyepecaller made heterozygous calls where there is no support for them in the BAM. We use IGV to compare input BAM and Haptyepecaller output bam. The region shown in the figure...
View ArticleShort read data in highly repetitive genomic region for heterozygous individuals
Hello GATK team, This might be a very general and overrated question but I appreciate your input. I am working with natural populations of plants (expected highly heterozygous individuals) and an...
View ArticleDistribution of RGQ scores
I work with non-human genomes and commonly need the confidence of the reference sites, so I was happy to see the inclusion of the RGQ score in the format field of GenotypeGVCFs. However, I am a little...
View ArticleIssue of Haplotype call on a large chromosome (>536 Mb)
Hi I tried to run HaplotypeCaller with GVCF mode. My reference genome is over 5 Gb in size. Below my code and error, Using GATK jar /source/gatk-4.0.6.0/gatk-package-4.0.6.0-local.jar Running: java...
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Mutect2 missed variant called by HaplotypeCaller
Hi, I am running GATK 3.5.0 with java version 1.8.0. I have two cell line samples that I paired with a promega baseline reference (its essentially a mixed germline sample) to run Mutect2 (which I am...
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 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 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 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...
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