Go Back   SEQanswers > General

Similar Threads
Thread Thread Starter Forum Replies Last Post
Help with variant calling pipeline Al'Thor Bioinformatics 3 06-04-2015 05:09 AM
Tumor-only variant calling etal Bioinformatics 1 12-05-2014 09:49 PM
Variant Calling with mpileup asebastian Bioinformatics 0 03-31-2013 08:53 PM
variant calling kjaja Bioinformatics 1 11-04-2011 07:16 AM

Thread Tools
Old 04-05-2018, 03:30 AM   #1
Junior Member
Location: Nottingham

Join Date: Apr 2018
Posts: 1
Default Variant calling using CRISP

I'm new to bioinformatics, and to the SEQ answers forum as well.
I am trying to analyze NGS data for 8 pools of 12 samples each. I am currently stuck at variant calling as CRISP seems to not detect any variants.
I have altered the minimum base quality (I have used mbq of 10 to 30) and minimum mapping quality. I suspect the problem may be from my reference sequence as I get this output which says
"reading chromosome chr13 offset 412481050"... and I suspect this isnot right because I am working with the APOE locus which is on chromosome 19.

Please how may I resolve this?
Aristotle is offline   Reply With Quote

crisp, ngs analysis, variant calling

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:52 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO