NGS Chew

“Tasty, tasty NGS Data!”

NGS Chew is a growing toolbox of software for running quality control and sanity checks on NGS. NGS chew can:

• Create a variant fingerprint file from BAM and VCF/BCF files.
  • The fingerprint files are store efficiently as compressed numpy arrays.
  • Optionally, allele balance information can be stored which enables advanced analysis downstream.
• Compare such fingerprint files to others to detect sample swaps and cryptic relationships.
• Analyze balance-enhanced fingerprint files for detecting cross-sample contamination.

Installation

Make sure samtools and bcftools are installed.

Quickstart

The following will create a sample.npz fingerprint file from the given BAM file.

ngs-chew fingerprint \
    --reference REFERENCE.fasta \
    --output-fingerprint sample.npz \
    --input-bam INPUT.bam \
    --genome-release GRCh37