freyja extract

Extracts reads from INPUT_BAM containing one or more QUERY_MUTATIONS

freyja extract [OPTIONS] QUERY_MUTATIONS INPUT_BAM

Options

--output <output>

path to save extracted reads

Default:

extracted.bam

--same_read

include to specify that query reads must all occur on the same read

Default:

False

Arguments

QUERY_MUTATIONS

Required argument

INPUT_BAM

Required argument

---

Example Usage:

The above command will extract reads containing one or more mutations of interest and save them to [input-bam]_extracted.bam. Additionally, the --same_read flag can be included to specify that all query mutations must occur on the same set of paired reads (same UMI).

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)