Hello All, I want to convert TCGA MAF to VCF analysis with PLINK I worked on the conversion of MAF2VCF using maf2vcf.pl, I got converted VCF file, but while conversion it has missing phenotype data and some gene id. due to this I could not able to process with PLINK analysis. please suggest me to exact conversation or adding phenotype data. Thank you.
To better help, you should show all commands that you have used.
Some general advice: when converting a VCF to PLINK format, PLINK will not know what are the phenotypes. You need to create a custom FAM file that matches exactly to the order of samples in your PLINK object - you can then use this FAM file in all downstream analysis via the
--fam command line parameter.
Please note: PLINK will NOT store your samples in the same order as they appear in the VCF. You can control this, however, via the
--indiv-sort file parameter when converting. Please read my previous answer, here: linkage disequilibrium analysis