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GenotypeGVCFs - Sites missing
I'm trying to call genotypes at a set of given positions from ~5,000 samples. To do so, I first generate gvcf files using HaplotypeCaller for the region around a gene for all samples separately with HaplotypeCaller. Then I'm merging the single gvcf files into batches of 1000 and then I'm generating the genotypes at ~180 sites using GenotypeGVCFs and the flag --includeNonVariantSites. Everything runs without errors, but in the end I noticed that ~20 sites were missing from the final VCF file. I then looked into these sites and the single files in detail and found out that there are simply no genotypes called for some samples at some positions.
I attached a small example. When I'm running the following command, no variant is in the output file:
java -jar GenomeAnalysisTK.jar \ -R hg19.fa \ -L region.bed --includeNonVariantSites \ -T GenotypeGVCFs \ --variant wrong.gvcf --variant correct.gvcf \ -o out.vcf
The same command works when running it with only "correct.gvcf" as an input, but obviously not when running it with only "wrong.gvcf". I noticed that wrong.gvcf might show a variant at this exact position.