HaplotypeCaller - christianparobek/cambodiaWGS GitHub Wiki

#####09 September 2015 Decided yesterday to try and make HaplotypeCaller work for our samples. Ran a batch HC to make g.vcf files for all P. falciparum samples yesterday. Eventually got it so that HC ran fine on individual samples, but the next step is to make a single multiVCF using GenotypeGVCFs. That's what I've worked on today - all day trying to figure out why it's hanging and crashing out of memory. Finally on to something. There is a parameter to both HaplotypeCaller and GenotypeGVCFs - --max_alternate_alleles - and this might be what is causing trouble. Default value is 6.