samtools-targetcut - Man Page

cut fosmid regions (for fosmid pool only)


samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0] [-1 em1] [-2 em2] [-f ref] in.bam


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)].


-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.


Written by Heng Li from the Sanger Institute.

See Also


Samtools website: <>

Referenced By


7 April 2022 samtools-1.15.1 Bioinformatics tools