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.