Troubleshooting

Multiple ALTs

There is an unaccounted for edge case in which a single variant has multiple ALT values. In this case, the counts for numbers of hom_ref, het, etc. will be wrong (or the script might just fail). Christian could not find a variant where this was the case, and thus was not sure exactly how the underlying data (in the VCF file) are represented in this case. If someone can find a variant with multiple ALTS, it should be relatively easy to update the aggregate_vcf.py script to handle this.