filterSomatic

Filter SNVs or Indels based on non genotype specific quality parameters.

Takes a vcf as its input and generates filtered vcfs as its output. Filtering can greatly reduce a vcf in size. This allows a vcf to be loaded into R or Python with reasonable memory usage, were complex genotype filtering can be performed.

Filtering is performed on several parameters:

• FILTER field in vcf
• Remove all SNVs or Indels
• QUAL
• Max alleles
• Chromosomes
• MQ
• Blacklists

USAGE:

python filterSomatic.py -i filterSomatic.ini

An example ini file is provided.

Dependencies

• Python >= 3.6.5
• vcftools >= 0.1.15
• snpeff >= 4.1
• coreutils >= 8.30 (Standard unix tools)