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TCGA legacy archive, muTect v119?
I want to reproduce some of the .vcf files I got from TCGA legacy archive from their .bam files. The headers included the following line:
I wonder if it indicates the MuTect version is
1.1.9 because the distributed version from CGA is
1.1.4, GATK hosts
1.1.7. Googled for v1.1.9 only saw people mentioning v1.1.7 or earlier.
Also, the current TCGA pipeline involved MuTect2. However one difference I noticed was that MuTect2 would give each record the value:
##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele fraction of the event in the tumor">
with almost default parameters. A vcf file from TCGAlegacy would instead include:
##FORMAT=<ID=FA,Number=.,Type=Float,Description="Fractions of reads (excluding MQ0 from both ref and alt) supporting each reported alternative allele, per sample">
So I guess it was not a version2 they used? If I can't get a v1.1.9 (i.e. assuming it was a tweaked version by TCGA team), could v1.1.7 or v2 be a equivalent tool? (I'm reproducing the germline callings, so somatic filter seems don't matter too much here)