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Old 10-15-2014, 03:18 PM   #3
Location: US

Join Date: Jun 2014
Posts: 34

I tried vcf-isec and it did not seem to work.

I was eventually able to install and setup vcftools, including sorting, indexing, and compressing the vcf files with tabix and bgzip.

The vcf-isec command gave a warning that column names do not match (i.e. 1-Normal and 1-Tumor). The command ran, but the output vcf file was 28 bytes of unreadable characters. Each of the 11 input files are around 80kb.

These are vcf files generated using MuTect (for comparing tumor to normal samples).

I am not sure if vcf-isec will work with MuTect vcf files or if there is something I am doing wrong. Maybe I can process the files ahead of time to get them to work.

The idea is that MuTect gives a list of somatic mutations in cancer samples by comparing to matched normal samples. What I am trying to do is take several MuTect vcf files, and see which variants are present in multiple vcf files or the 'intersection.'
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