TCGA SNP to plink

Question

[Omics data mining]

Hello everyone

I want to convert from TCGA SNP to PLINK. Can anyone suggest here

1. I downloaded MAF files from https://gdac.broadinstitute.org/ . Is it OK if I follow conversion MAF to VCF to PLINK ?

2. 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

Archana

[Gabriel R.]

Could you send a direct link to the MAF file you want to convert?

[Omics data mining]

Hi

Here is Data link http://firebrowse.org/?cohort=PAAD I downloaded Mutation_Packager_Oncotated_Calls (MD5) under Mutation Annotation File.

Thanks

Archana

[Kevin Blighe]

If you have MAF, you do not have to convert to VCF for the purposes of inputting to PLINK. Please see this recent answer, where I helped a user get their Illumina data into PLINK format: A: recode SNPs ATGC illumina

Please look up the PLINK input formats and then look at your MAF data to see what you need. You will likely need the lfile format that I eventually used for the gy in the other thread.