Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Make GATK tool to sort non-VCF reference-ordered files #2197

chandrans opened this issue Oct 6, 2016 · 0 comments


None yet
2 participants
Copy link

commented Oct 6, 2016

Feature request

Tool(s) involved

New tool for generating properly sorted non-VCF reference-ordered files (i.e. refseq).


There was a script that did this for refseq files, but it was deprecated. Users have asked for the script, but it is best to make a new tool to do this instead of providing an external script. For example, we may have refseq files where entries are not ordered by reference position. This tool should re-order entries according to a sequence dictionary, like what Picard SortVcf does for VCFs, but for generic ROD formats.

This Issue was generated from your forums

@chandrans chandrans added the Vanilla label Oct 6, 2016

@droazen droazen added community-request and removed Vanilla labels Mar 22, 2017

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.