I have a vcf file created with GATK with spanning deletion https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele- and I now need to compare this VCF with its gold standard using hap.py (https://github.com/Illumina/hap.py/blob/master/doc/happy.md#getting-started) but the spanning allele gives me the following error:
[W] too many AD fields at chr10:133017183 max_ad = 2 retrieved: 3
and I've read that is due to * in the ALT column.
So, is there a way to convert the spanning alleles into simple vcf files?
Thanks a lot, Denise
rtg-tools vcfeval
since it's designed to account for differences in indel representation between the truthset and callset. $\endgroup$