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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.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

Ignore bases with quality less than minBaseQ.

Penalty for in state transition.
-0 em0
Emission score 0.
-1 em1
Emission score 1.
-2 em2
Emission score 2.
Reference FASTA file.

AUTHOR

Written by Heng Li from the Sanger Institute.

SEE ALSO

samtools(1)

Samtools website: <http://www.htslib.org/>

15 April 2024 samtools-1.20