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nmdp-bioinformatics / pipeline

Consensus assembly and allele interpretation pipeline.
GNU Lesser General Public License v3.0
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can upgrade to post-HTSlib version of samtools and bcftools, here on github #32

Closed ybolon-nmdp closed 9 years ago

ghost commented 10 years ago

I'm not sure exactly what is meant by this issue report, but the latest version of bcftools and samtools supported by homebrew-science is version 1.1 last updated on 23 Sept 2014.

https://github.com/Homebrew/homebrew-science/blob/master/bcftools.rb https://github.com/Homebrew/homebrew-science/blob/master/samtools.rb

ybolon-nmdp commented 10 years ago

Lines in process_fastq.sh would change with use of latest versions.

ghost commented 9 years ago

I don't believe homebrew-science is currently the source of bcftools and samtools in the private cloud or on AWS, so they are mostly likely out of date.

If we were to update to version 1.1 or later, process_fastq.sh would need to change to something similar to https://github.com/nmdp-bioinformatics/flow/blob/master/assemble.nf#L87 https://github.com/nmdp-bioinformatics/flow/blob/master/assemble.nf#L120