chimera (version 1.14.0)

filterSamReads: A function to filter SAM or BAM files

Description

A function to filter SAM or BAM files using picard-tools

Usage

filterSamReads(input, output, filter=c("includeAligned","excludeAligned"))

Arguments

input

SAM/BAM file to be validated

output

file name in which to save the filtered reselts

filter

type of filter

Value

A filtered SAM/BAM.

See Also

picardInstallation

Examples

#	filterSamReads(input="kd2_accepted_hits2.sam", output="kd2_accepted_hits2_mapped.sam", filter="includeAligned")