Man page - samtools-targetcut(1)
Packages contains this manual
- samtools-head(1)
- samtools-reference(1)
- samtools-addreplacerg(1)
- samtools(1)
- samtools-collate(1)
- samtools-fixmate(1)
- samtools-cat(1)
- samtools-markdup(1)
- samtools-targetcut(1)
- samtools-tview(1)
- wgsim(1)
- samtools-samples(1)
- samtools-split(1)
- samtools-sort(1)
- samtools-index(1)
- samtools-coverage(1)
- samtools-dict(1)
- samtools-import(1)
- samtools-cram-size(1)
- ace2sam(1)
- samtools-bedcov(1)
- samtools-flagstat(1)
- samtools-reheader(1)
- samtools-depth(1)
- samtools-flags(1)
- samtools-phase(1)
- samtools-view(1)
- samtools-merge(1)
- samtools-rmdup(1)
- samtools-fqidx(1)
- samtools-fasta(1)
- samtools-fastq(1)
- samtools-quickcheck(1)
- samtools-calmd(1)
- samtools-mpileup(1)
- samtools.pl(1)
- samtools-consensus(1)
- samtools-depad(1)
- samtools-ampliconstats(1)
- samtools-faidx(1)
- samtools-ampliconclip(1)
- samtools-reset(1)
- samtools-idxstats(1)
- samtools-stats(1)
apt-get install samtools
Manual
samtools-targetcut
NAMESYNOPSIS
DESCRIPTION
OPTIONS
AUTHOR
SEE ALSO
NAME
samtools-targetcut - cut fosmid regions (for fosmid pool only)
SYNOPSIS
samtools targetcut [ -Q minBaseQ ] [ -i inPenalty ] [ -0 em0 ] [ -1 em1 ] [ -2 em2 ] [ -f ref ] in.bam
DESCRIPTION
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
-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. |
AUTHOR
Written by Heng Li from the Sanger Institute.
SEE ALSO
samtools (1)
Samtools website: <http://www.htslib.org/>