samtools-targetcut - cut fosmid regions (for fosmid pool only)
samtools targetcut [
-Q minBaseQ] [
-i inPenalty]
[
-0 em0] [
-1 em1] [
-2 em2]
[
-f ref]
in.bam
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)].
-
-Q minBaseQ
- Ignore bases with quality less than minBaseQ.
-
-i inPenalty
- Penalty for in state transition.
-
-0 em0
- Emission score 0.
-
-1 em1
- Emission score 1.
-
-2 em2
- Emission score 2.
-
-f ref
- Reference FASTA file.
Written by Heng Li from the Sanger Institute.
samtools(1)
Samtools website: <
http://www.htslib.org/>