Man page - samtools-targetcut(1)
Packages contas this manual
- samtools-cram-size(1)
- samtools-addreplacerg(1)
- samtools-mpileup(1)
- ace2sam(1)
- wgsim(1)
- samtools-consensus(1)
- samtools-phase(1)
- samtools(1)
- samtools-reset(1)
- samtools-ampliconclip(1)
- samtools-depth(1)
- samtools-flagstat(1)
- samtools-coverage(1)
- samtools-dict(1)
- samtools-head(1)
- samtools-sort(1)
- samtools-flags(1)
- samtools-fastq(1)
- samtools-ampliconstats(1)
- samtools-calmd(1)
- samtools-bedcov(1)
- samtools-index(1)
- samtools-merge(1)
- samtools-fasta(1)
- samtools-fqidx(1)
- samtools-collate(1)
- samtools-view(1)
- samtools-split(1)
- samtools-quickcheck(1)
- samtools-samples(1)
- samtools-idxstats(1)
- samtools-fixmate(1)
- samtools-reheader(1)
- samtools-rmdup(1)
- samtools-markdup(1)
- samtools-targetcut(1)
- samtools-depad(1)
- samtools-tview(1)
- samtools-faidx(1)
- samtools-stats(1)
- samtools.pl(1)
- samtools-import(1)
- samtools-cat(1)
- samtools-reference(1)
Package: samtools
apt-get install samtools
apt-get install samtools
Manuals in package:
Documentations in package:
Manual
| samtools-targetcut(1) | Bioinformatics tools | samtools-targetcut(1) |
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/>
| 12 September 2024 | samtools-1.21 |