Pipeline Steps - Variant Intersection

If two or more algorithms were selected the Intersect workflow will run. Currently the resulting VCF and MAF files include any SNVs found by two or more algorithms.

BCFtools isec -n +1; VennDiagram

Determines presence/absence of each SNV within each algorithm's set of filtered SNVs. Results are listed in the output files: isec-1-or-more/README.txt and isec-1-or-more/sites.txt, and are summarized in a Venn Diagram plot (TIFF format).

BCFtools isec -n +2

Determines presence/absence of SNVs found in two or more of each algorithm's set of filtered SNVs, and outputs a consensus VCF for each algorithm containing SNVs found by that algorithm plus at least one other algorithm. Results are also listed in the output files: isec-2-or-more/README.txt and isec-2-or-more/sites.txt.

BCFtools concat

Concatenates the 2+ algorithm consensus SNVs into one VCF (SNV-concat.vcf.gz). The output header is a uniquified concatenation of all input VCF headers. The output fields INFO, FORMAT, NORMAL and TUMOR are from the first listed VCF that has the SNV. Input VCFs are sorted alphanumerically by the algorithm name.

vcf2maf

Converts SNV-concat.vcf.gz from step 3 into MAF format. Output includes allele counts and flanking basepairs, but most fields are blank. Details can be found here.