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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.
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