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| 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.bamDESCRIPTION
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/>
| 21 February 2022 | samtools-1.15 |
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