SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
undescribed snpEff error after command execution MGCBrown Bioinformatics 1 05-25-2017 12:18 PM
MirDeep 2 fail during execution of miRDeep2.pl RTK45 Bioinformatics 4 12-10-2013 05:38 AM
Problems with blastn execution from command line angeloulivieri Bioinformatics 1 10-03-2012 03:48 AM
BioPerl installation and execution problem shrujan Bioinformatics 1 08-17-2012 05:02 AM
Error in Galaxy tool execution? nilmot13 Bioinformatics 2 01-26-2012 03:34 AM

Reply
 
Thread Tools
Old 01-11-2020, 04:52 AM   #1
cmccabe
Senior Member
 
Location: chicago

Join Date: Jul 2012
Posts: 354
Default optimize a execution of a pindel process

I am looking to optimize a pindel process. Below is the command used:

Code:
pindel -f refererence -i configfile -c ALL -T 16 -o sample
I then execute pindel2vcf on the output.... I was thinking of adding

Code:
samtools view -h -F 0x900 <bam>
before making the configfile to filter or secondary and supplementary alignments. My thinking is that pindel will be able to use the primary alignments better without these other alignments slowing it down, is that true or is there a better option? Thanks
cmccabe is offline   Reply With Quote
Reply

Tags
pindel

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 08:18 PM.


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