I recognized that in case of a reference call, MVCFA writes an 'N' in the alignment (SNP and complete genome). This only happens when using GATK3.8+. I fixed the corresponding lines in the code, however, did not test it systematically (but it seemed to have work for the analysis I did).
I recognized that in case of a reference call, MVCFA writes an 'N' in the alignment (SNP and complete genome). This only happens when using GATK3.8+. I fixed the corresponding lines in the code, however, did not test it systematically (but it seemed to have work for the analysis I did).