ExAC frequencies are missing for some indels in the maf2maf output

[ShwetaCh]

Hi Cyriac,

In the maf2maf VEP output, indels such as 5 56177848 TCAA T are not getting populated with ExAC frequencies. However, the ExAC vcf ExAC_nonTCGA.r0.3.1.sites.vep.vcf does have this allele present in the file but in a non-normalized format : 5 56177848 . TCAACAACAACAA TCAACAACAA, and probably why it is not getting recognized.

-Shweta

[ckandoth]

Thanks for reporting this. This seems to be a bug in the ExAC plugin. See this line in their code. A fix seems simple, and we can send them a pull request. For each variant, tabix is used to pull overlapping lines in the ExAC VCF, and alleles are loaded in a list called @vcf_alleles. These are compared one-by-one against the input variant allele. But before that, they need to be normalized using a simple regex, or something like bcftools norm.

[ckandoth]

This is now handled in 86e58e3