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Michael T. Wolfinger > Bio-ViennaNGS > bam_uniq.pl

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NAME ^

bam_uniq.pl - Deconvolute BAM files into unique and multi mappers

SYNOPSIS ^

bam_uniq.pl [--bam FILE] [-o DIR] [options]

DESCRIPTION ^

This program extracts uniquely and multiply mapping reads from BAM files acoording to the NH:i SAM attribute and creates separate BAM files for unique and multi mappers, respectively.

OPTIONS ^

--bam

BAM file to extract unique and multi mappers from

--band

Process bands of (supposedly paired-end) reads sharing the same name/id from a name-sorted BAM file. The reads of band are considered unique mappers if and only if all of them are unique mappers. In all other cases, all reads of a band are considered multi mappers. In a paired-end context this means that e.g. a read map uniquely, but its mate is a multi-mapper, both will be consideres multi-mappers.

--out -o

Output path

--help -h

Print short help

--man

Prints the manual page and exits

AUTHOR ^

Michael T. Wolfinger <michael@wolfinger.eu>

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