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

  • $\begingroup$ Could you describe what problems you're having? You could try using rtg-tools vcfeval since it's designed to account for differences in indel representation between the truthset and callset. $\endgroup$
    – user438383
    Feb 23, 2021 at 15:16
  • $\begingroup$ Thanks a lot, I know I can use it but I would like to follow the best practises given by the Global Alliance for Genomics and Health Benchmarking Team (ncbi.nlm.nih.gov/pmc/articles/PMC6699627) $\endgroup$ Feb 23, 2021 at 16:03
  • $\begingroup$ Please edit your question and include some of the offending lines. Also make sure to include the relevant headers since the headers are where this sort of thing is defined. We can't really help without seeing the file. $\endgroup$
    – terdon
    Feb 27, 2021 at 18:42


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