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.

Sign up for GitHub

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

Jump to bottom

Suggestion: seqVCF2GDS could use index file to get total number of variants #53

Open
jemunro opened this issue Jul 1, 2019 · 0 comments
Open

Suggestion: seqVCF2GDS could use index file to get total number of variants #53

jemunro opened this issue Jul 1, 2019 · 0 comments
Assignees
@zhengxwen
Labels
feature required

Comments

@jemunro
Copy link

jemunro commented Jul 1, 2019

Generally VCF files are accompanied by an index file, and from this file the number of variants can be obtained. For example with bcftools: bcftools index --nrecords <in.vcf.gz>

This could be used to speed up the seqVCF2GDS function by avoiding the variant counting step. As this step is currently single threaded, it contributes significantly to the run-time when converting large VCF files.
@zhengxwen zhengxwen self-assigned this Jul 1, 2019
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@zhengxwen zhengxwen

Labels
feature required
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@zhengxwen @jemunro