I want to convert from TCGA SNP to PLINK. Can anyone suggest here
I downloaded MAF files from https://gdac.broadinstitute.org/ . Is it OK if I follow conversion MAF to VCF to PLINK ?
If yes, I worked on the conversion of MAF2VCF using maf2vcf.pl , but for every MAF file, I am getting this warning
WARNING: Reference allele mismatches found. Storing them here for debugging: JSN/gdac.broadinstitute.org_PAAD.Mutation_Packager_Calls.Level_3.2016012800.0.0/TCGA-2J-AAB1-01.vcf/TCGA-2J-AAB1-01.maf.skipped.tsv
Most of the data information is getting lost and I cannot process. I have used Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz reference version. Can anybody suggest what I should do to fix this warning ?? From many days, I am trying to fix this issue, but still no output.
I will appreciate all suggestions