I have already removed the information in the INFO and FORMAT except from the GT. Due to the error, I thought of pre.py. When I run pre.py, I receive a VCF that contains calls with invalid genotype[s] (non existent allele) at chr12:119344875.
Do I have to filter them out one by one in order to use hap.py?
When I run hap.py with an already reduced TRUTH_VCF and QUERY_VCF, I get the following error:
I have already removed the information in the INFO and FORMAT except from the GT. Due to the error, I thought of pre.py. When I run pre.py, I receive a VCF that contains calls with invalid genotype[s] (non existent allele) at chr12:119344875. Do I have to filter them out one by one in order to use hap.py?
Help would be much appreciated!