I'm a beginner in bioinformatics.
in TCGA data portal, there are 5 types of TCGA.BRCA.MAF (https://portal.gdc.cancer.gov/repository/ *not legacy archive)
I am interested in these files:
(all of maf files have same samples)
TCGA.BRCA.mutect.053f01ed-3154-4aea-9e7f-932c435034b3.DR-10.0.protected.maf.gz TCGA.BRCA.muse.b8ca5856-9819-459c-87c5-94e91aca4032.DR-10.0.somatic.maf.gz TCGA.BRCA.mutect.995c0111-d90b-4140-bee7-3845436c3b42.DR-10.0.somatic.maf.gz TCGA.BRCA.somaticsniper.7dd592e3-5950-4438-96d5-3c718aca3f13.DR-10.0.somatic.maf.gz
I want to merge/combine 5 maf files to single maf file rather than choose only one
I have two cases in mind.
1- remain only mutations reported by at least 2(or 3) maf files (callers) 2- remain all mutation but, de-duplicate (solving the problem by the same sample)
Is there any tool I can use in this situation? or any document?