Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Filtering steps for VarScan2 somatic and germline calls ElenaN Bioinformatics 4 08-27-2014 04:57 AM
Interpreting Pindel output bwubb Bioinformatics 11 07-07-2014 05:47 AM
Mutect for miRNA somatic calls? ninad Bioinformatics 0 09-02-2013 07:59 PM
Pindel- empty output? Seq_student Bioinformatics 12 08-15-2013 12:30 PM
understanding pindel output frymor Bioinformatics 1 01-22-2013 01:44 PM

Thread Tools
Old 04-28-2014, 11:58 AM   #1
Junior Member
Location: San Jose, CA

Join Date: Oct 2013
Posts: 6
Default Filter somatic calls in Pindel output

I'm running Pindel on some normal/tumor pairs. A lot of calls seem to be germline. Is there a filtering script out there to get the somatic calls?
persorrels is offline   Reply With Quote
Old 04-29-2014, 07:23 AM   #2
Senior Member
Location: amsterdam

Join Date: Jun 2009
Posts: 133

You could do an awk selection based on the number of samples and the numbers of reads supporting the ALT. then filtering dbSNP entries and restrict homopolymer and micro satellite calls to regions called somatic by MSIsensor.
KaiYe is offline   Reply With Quote

filter, pindel, somatic

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 10:49 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO