Awesome

TCGA_germline-nf

extraction of germline variants from TCGA data

Dependencies

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

Description

This program takes in input a TCGA data-like folder of VCF files, e.g. myfolder containing all /ids_sample1/sample1.vcf, /ids_sample2/sample2.vcf, /ids_sample3/sample3.vcf, etc.
Then it filters out germline variants from these VCF files, with a minimum coverage --min_DP and variant allelic fraction --min_af.
After that it reformats these files into annovar inputs (by cancer type) and output them in a result folder (--out_folder).

Execution

Nextflow seamlessly integrates with GitHub hosted code repositories:

nextflow run iarcbioinfo/TCGA_germline-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_germline-nf --help