Editing
EricChu:LabNotesMDA/2015-11-10
(section)
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
==Extract All Unmatched SNV after Ref Correction== $ perl /home/ericchu/softwares/removeduplicateline.pl PGP1_21_ch15.unique.HLA0.mismatch18nCGI.vcf PileupCh15HLA0mismatchCh18complement.txt PGP1_21_ch15vcfunmatched.txt $ wc -l PGP1_21_ch15vcfunmatched.txt 531 PGP1_21_ch15vcfunmatched.txt (Still 5 uncertain from alignment) * remove low quality $ perl /home/ericchu/softwares/removelowquality30.pl PGP1_21_ch15vcfunmatched.txt PGP1_21_ch15vcfunmatched.quality.txt $ wc -l PGP1_21_ch15vcfunmatched.quality.txt 252 PGP1_21_ch15vcfunmatched.quality.txt $ perl /home/ericchu/softwares/removeduplicateline.pl PGP1_21_ch18.unique.HLA0.mismatch15nCGI.vcf PileupCh18HLA0mismatchCh15complement.txt PGP1_21_ch18vcfunmatched.txt $ wc -l PGP1_21_ch18vcfunmatched.txt 407 PGP1_21_ch18vcfunmatched.txt * remove low quality $ perl /home/ericchu/softwares/removelowquality30.pl PGP1_21_ch18vcfunmatched.txt PGP1_21_ch18vcfunmatched.quality.txt $ wc -l PGP1_21_ch18vcfunmatched.quality.txt 135 PGP1_21_ch18vcfunmatched.quality.txt * However a lot of them have good base quality but very low depth (DP) chr6 30523430 . C G 30 0 DP=1 GT:GQ:DP 1/1:30:1 chr6 30538637 . T A 75 0 DP=11 GT:GQ:DP 0/1:75:11 chr6 30544307 . C T 114 0 DP=16 GT:GQ:DP 0/1:64:16 chr6 30546029 . A G 30 0 DP=1 GT:GQ:DP 1/1:30:1 chr6 30546679 . A G 30 0 DP=1 GT:GQ:DP 1/1:30:1 chr6 30547425 . G A 30 0 DP=1 GT:GQ:DP 1/1:30:1 chr6 30547443 . C T 30 0 DP=1 GT:GQ:DP 1/1:30:1 chr6 30547523 . A T 33 0 DP=2 GT:GQ:DP 1/1:33:2 chr6 30548506 . A T 30 0 DP=1 GT:GQ:DP 1/1:30:1 chr6 30548776 . A G 30 0 DP=1 GT:GQ:DP 1/1:30:1 chr6 30548786 . T C 30 0 DP=1 GT:GQ:DP 1/1:30:1 chr6 30548795 . C T 30 0 DP=1 GT:GQ:DP 1/1:30:1 chr6 30551806 . A G 34 0 DP=3 GT:GQ:DP 0/1:1:3 chr6 30551807 . A G 34 0 DP=3 GT:GQ:DP 0/1:1:3 chr6 30555369 . G A 63 0 DP=13 GT:GQ:DP 1/1:26:13 chr6 30556424 . C T 35 0 DP=5 GT:GQ:DP 0/1:35:5 chr6 30556814 . C T 33 0 DP=2 GT:GQ:DP 1/1:33:2 ... * If DP equals or large than 5, then unmatched in chamber 15 and 18 would drop to 149 SNVs and 36 SNVs respectively. [[File:VennDiagramHLAP2&CompleteGenomics3.jpg|800px]]
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information