samtools-targetcut1
Cut fosmid regions (for fosmid pool only)
Usage
samtools targetcut
[-Q
minBaseQ]
[-i
inPenalty]
[-0
em0]
[-1
em1]
[-2
em2]
[-f
ref]
in.bam
Overview
This command identifies target regions by examining the continuity of read depth, computes haploid consensus sequences of targets and outputs a SAM with each sequence corresponding to a target. When option -f is in use, BAQ will be applied. This command is only designed for cutting fosmid clones from fosmid pool sequencing [Ref. Kitzman et al. (2010)].
Options
|
Ignore bases with quality less than minBaseQ. |
|---|---|
|
Penalty for in state transition. |
|
Emission score 0. |
|
Emission score 1. |
|
Emission score 2. |
-
-f ref -
Reference FASTA file.
Releases
3 releases since Debian 11 (Bullseye); the text changed 2 times.