Cannot Find a bamUtil Version with "dedup_LowMem --allReadNames" Option

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Bren K

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Oct 16, 2019, 4:58:52 AM10/16/19

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Hi,

I’m trying to harmonize my project’s data with TOPMed (https://www.nature.com/articles/s41467-018-06159-4#Sec7), but cannot a find version of bamUtil with an “--allReadNames” option. I have tried both conda installs however both do not contain the “--binCustom” optiong. The version on your website does have the “binCustom”, but not the “allReadNames”.

Is there a version available with this option? The Reiger paper links to this docker with the full BQSR command, is there a way I can use this version? https://github.com/statgen/docker-alignment

bamUtil (October 16):

wget https://github.com/statgen/bamUtil/archive/v1.0.14.tar.gz

Conda Install (October 16):

conda install -c bioconda bamutil

conda install -c bioconda/label/cf201901 bamutil

Best,

Brendan Kenna

Bren K

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Oct 16, 2019, 5:05:32 AM10/16/19

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I also just tried the latest version of "gotCloud" and it also does not contain the "binCustom" and "allReadNames" options