Expected file size - Haplotype Caller

bvecchio

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

Geraldine_VdAuwera

Hi there,

Can you clarify -- is the run completing "successfully" (the program finishes without error message) or are you saying you're not seeing anything when you look in the file after some hours but before the run is complete?

bvecchio

The run completes successfully, without errors. I view the file after completion, and there is no data other than the header.

Geraldine_VdAuwera

I see. Have you tried running on a subset of your file? Since you're working with an exome, I assume you have target intervals? You can pass those with -L; if your problem is due to file size that may work around it.