Variation in MAF formats

[jashapiro]

File(s)

pbta-snv-strelka2.vep.maf.gz
pbta-snv-lancet.vep.maf.gz
pbta-snv-mutect2.vep.maf.gz
pbta-snv-vardict.vep.maf.gz

Release

v9

Link to OpenPBTA-manuscript

https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/master/content/03.methods.md#vcf-annotation-and-maf-creation

Question/issue

The maf files included in v9 do not have consistent columns.
In most, there is a variant_id and variant_qual column (though whether there is any content in those is still variable); but in pbta-snv-strelka2.vep.maf.gz, there are instead vcf_id, vcf_qual, and vcf_pos.

It seems this is likely due to the files being processed with different versions of vcf2maf.pl:
mskcc/vcf2maf@051aaaf
Rerunning the current version of vcf2maf.pl on all files should solve this.

[jharenza]

updated with #273