Hi Christian, all this functionality is available either in the picard tools or in the samtools collection. bam_filter is also available and based on bam_utils. There is also a suite of bam-tools. So many tools to choose from :) Hope this helps, Bjoern Am 26.02.2016 um 17:35 schrieb Christian Brenninkmeijer:

Hi All,

Has anyone written galaxy tools for the samtools view functions such as

samtools view -f 0x0002 -F 0x0100 -uo

and/or

samtools view -uSo

Thanks Christian University of Manchester

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