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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
       -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/>

samtools-1.11		       22 September 2020	 samtools-targetcut(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO

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