Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Counting coverage bases batsal Bioinformatics 0 02-17-2012 11:46 AM
Fragment Size shift on Egel bye using the new TrueSeq protocol ? Claire1 Illumina/Solexa 7 05-11-2011 08:01 AM
Fragment Size shift on Egel bye using the new TruSeq protocol ? Claire1 Sample Prep / Library Generation 2 05-05-2011 01:37 PM

Thread Tools
Old 06-18-2012, 11:29 AM   #1
Junior Member
Location: Vancouver BC. Canada

Join Date: Jun 2012
Posts: 2
Question VarScan shift in counting of bases!

I'm using VarScan.v2.2.11.

The problem I'm reporting here is something about VarScan's parameter --min-avg-qual when using command mpileup2indel. I'm setting it to be default, which is 15.

In the input pileup file:
CHROMOSOME_I 221154 g 42 .,,,,,,,+1c,+1c,,+1c,+1c,+1c,+1c,+1c,+1c,+1c,+1c,+1c,+1c,+1c.+1C,+1c.+1C,+1c,+1c,+1c,+1c.+1C.+1C,+1c,+1c,+1c.+1C,+1c,+1c,+1c.+1C.+1C.+1C.+1C.+1C 1C?C<FFFFDHJEAJDJIJG<JJG'GIDIJBD9JDDDG?FDF

The corresponding output:
CHROMOSOME_I 221154 G +C */+C:41:8:34:45.33%:4.4044E-13 Pass:11:30:10:24:1E0 0 1 0 0 */+C:41:8:34:45.33%:4.4044E-13

The red colored part of the input won't get passed the --min-avg-qual filteration, because it's base quality is less than 15. The prblem is that in the output, we see the Cov=41 (which is correct), Reads1=8 (which is also correct), but Reads2=34 (which should be 33, because one of the insertion has mapping quality less than 15).

Anyone has a similar problem like me? Could anyone help? I think this might be a bug of VarScan.
AlbertZANG is offline   Reply With Quote

mpileup, varscan

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 07:33 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO