'setFile' format 0-based or 1-based ? refFlat: only exons ?

[lindenb]

Hi, thank your for writing rvtests.

A quick question: if the setFile format

• half-closed 0-based like bed ?
• or open 1-based like gtf/gff ?

And in the refFlat format: do you only consider the exons or the whole transcript (including introns) ?

thank you.

[dajiangliu]

VCF is following 1-based, and we are following that. Thanks!

All the best, Dajiang

Associate Professor Co-Chair, Bioinformatics and Genomics Graduate Program Dept. Public Health Sciences Institute of Personalized Medicine Penn State College of Medicine, ASB 4301C Email: @.*** URL: https://dajiangliu.blog https://dajiangliu.blog Tel: +1-717-531-4178

On Mon, Jan 17, 2022 at 12:24 PM Pierre Lindenbaum @.***> wrote:

Hi, thank your for writing rvtests.

A quick question: if the setFile format

• half-closed 0-based like bed ?
• or open 1-based like gtf/gff ?

?

thank you.

— Reply to this email directly, view it on GitHub https://github.com/zhanxw/rvtests/issues/130, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACNCDJIU7PVL3PO2MOMJ2ITUWRGF3ANCNFSM5MFHAVDQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you are subscribed to this thread.Message ID: @.***>