Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Expected file size - Haplotype Caller

bvecchiobvecchio Posts: 4Member
edited October 2012 in Ask the team

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 header of the VCF - no errors seen. I'm wondering if this is due to limited space on my drives or if the expected file size is much larger than I am anticipating.

Command:

GenomeAnalysisTK.jar -T HaplotypeCaller -R  Homo_sapiens_assembly19.fasta -I input.bam --dbsnp dbsnp_132.b37.nochr.vcf  -stand_call_conf 30 -stand_emit_conf 10 -o output.Haplotypes.vcf
Post edited by Geraldine_VdAuwera on

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