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Filter SNVs or Indels based on non genotype specific quality parameters.
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README.md
filterSomatic.ini
filterSomatic.py

README.md

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)
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