crystal facets

Crystal implementation of FACETS as a command-line tool.

Status

• Crystal only
• CLI first
• Internal snp-pileup based on HTSlib
• Baseline implementations of preprocessing, segmentation, clustering, and CN fitting

Install

shards build --release

Commands

Show help:

bin/facets help

Generate FACETS pileup CSV from VCF and BAM or CRAM input:

bin/facets pileup sites.vcf normal.bam tumor.bam -o sample.csv

Run preprocessing and write jointseg TSV:

bin/facets preproc sample.csv.gz -o jointseg.tsv --pmat pmat.tsv

Run preprocessing and segment summarization:

bin/facets proc-sample sample.csv.gz -o segments.tsv --jointseg jointseg.tsv

Input

The minimum required columns for SNP matrix input are:

• chrom
• pos

Accepted aliases:

• chrom, chr, chromosome
• pos, position, loc

Typical optional columns:

• nor_dp
• nor_rd
• tum_dp
• tum_rd
• vaf_n
• vaf_t
• gcpct

FACETS pileup CSV input is also supported.

Library

require "./src/facets"

table = Facets::IO::ReadSnpMatrix.read("example.csv")
result = Facets::Preprocess::PreProcSample.call(table)
pp result.jointseg.chrom_ranges

rows = Facets::IO::SnpPileup.call("sites.bcf", ["normal.bam", "tumor.bam"])
pp rows.first.to_csv_line