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.
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-0 em0 |
Emission score 0. |
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-1 em1 |
Emission score 1. |
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-2 em2 |
Emission score 2. |
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-f ref |
Reference FASTA file. |
AUTHOR
Written by Heng Li from the Sanger Institute.
SEE ALSO
Samtools website: <http://www.htslib.org/>;