Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Sign In with Google Sign In with OpenID Sign In with Twitter
Sign In Register

Categories

Powered by Vanilla. Made with Bootstrap.
Service note: Geraldine is on vacation this week; other members of GSA will be responding to questions, but they have a lot of work besides this, so be aware that responses may be a little slower than usual. Thank you for your patience.

best practices and filter on small exome experiment

dcittarodcittaro Posts: 13Member ✭
in Ask the team

Hi all, I have a 4 exome experiment (high coverage). According to best practices I can't apply VQSR, so I must filter on SNP properties. One thing is not clear: should all the option apply? In other words should I select using boolean "and" (i.e. QD  < 2.0 & MQ < 40.0 & FS > 60.0 & HaplotypeScore > 13.0 & MQRankSum < -12.5 & ReadPosRankSum < -8.0 for SNP) or "or" (i.e. QD  < 2.0 | MQ < 40.0 | FS > 60.0 | HaplotypeScore > 13.0 | MQRankSum < -12.5 | ReadPosRankSum < -8.0 for SNP)?

Post edited by Geraldine_VdAuwera on
Tagged:
Flag • Off Topic Disagree Agree Like WTF •
Sign In or Register to comment.