Route: wes-pairs-snv

Somatic point mutations and small insertions/deletions for the wes or rna-snv results.

Usage

After individual samples are processed with the wes or rna-snv route, manually define tumor-normal sample pairs in the samples.pairs.csv sample sheet.

Run wes-pairs-snv route from the same directory as wes.

sns/run wes-pairs-snv

Output

Primary results:

• VCF-*: VCF files generated by Mutect and Strelka variant callers.
• VCF-*-annot.all.txt: Table of functionally annotated variants.
• VCF-*-annot.coding.txt: Table of coding region variants (subset of all variants).
• VCF-*-annot.nonsyn.txt: Table of non-synonymous, frameshift, and splicing variants (subset of coding variants).

Run metrics:

• summary.VCF-*-annot.csv: Number of mutations per sample for different variant callers.