freyja filter

Excludes reads from INPUT_BAM containing one or more QUERY_MUTATIONS between MIN_SITE and MAX_SITE (genomic coordinates)

freyja filter [OPTIONS] QUERY_MUTATIONS INPUT_BAM [MIN_SITE] [MAX_SITE]

Options

--output <output>

path to save filtered reads

Default:: filtered.bam

Arguments

QUERY_MUTATIONS: Required argument

INPUT_BAM: Required argument

MIN_SITE: Optional argument

MAX_SITE: Optional argument

Example Usage:

Excludes reads containing one or more mutations, akin to freyja extract but with the opposite effect.

[min-site] and [max-site] specify the range of reads to include. Formatting requirements for [query-mutations.csv] can be found below, where SNPs, insertions, and deletions are listed in separate lines.

C75T,G230A,A543C
(732:'TT'),(1349:'A'),(12333:'A')
(1443:32),(1599:2),(2036:3)