TCGA_platypus-nf

convert TCGA VCF into annovar-ready tables with nextflow

Dependencies

Install nextflow.

curl -fsSL get.nextflow.io | bash

And move it to a location in your $PATH (/usr/local/bin for example here):

sudo mv nextflow /usr/local/bin

Install vt, and put the executable in your PATH.

Install VCFtools, and put vcf-sort in your PATH.

Description

This program takes in input a folder of compressed VCF files, from variant calling on TCGA data : 10th column of header must be the TCGA sample barcode (see specification here).
It reformats these VCF into annovar input tables by cancer type and output them in a result folder (--out_folder). Caution: VCF must be zipped, with extension vcf.gz.

Execution

Nextflow seamlessly integrates with GitHub hosted code repositories:

nextflow run iarcbioinfo/TCGA_platypus-nf --TCGA_folder myfolder

Help and options

You can print the help manual by providing --help in the execution command line:

nextflow run iarcbioinfo/TCGA_platypus-nf --help