Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
how to compute all restriction enzyme sites in the human genome? lunacab General 10 07-09-2017 04:36 PM
Human Reference Genome Mucki0815 General 9 01-10-2013 12:08 PM
which human Reference genome to use david.tamborero Bioinformatics 4 12-22-2011 07:27 AM
12th International Meeting on Human Genome Variation and Complex Genome Analysis marcowanger Events / Conferences 1 08-29-2011 09:38 PM
Reference genome for MAQ - split reference genome by chromosome or not? inesdesantiago Bioinformatics 4 02-18-2009 09:44 AM

Thread Tools
Old 07-10-2012, 02:11 AM   #1
bioinf newbie
Location: India

Join Date: Feb 2012
Posts: 13
Default How to compute percentage of my genome covering human reference genome?

I have the alignment file for my genome (bam).
I want to find out % of genome that covered reference human genome with atleast 1 read, 2 reads, 3 reads, and 4 reads.
How do I go about it?
bioinf newbie is offline   Reply With Quote
Old 07-10-2012, 04:03 AM   #2
Location: Netherlands

Join Date: Sep 2009
Posts: 43

Maybe this can help you:

Requires some work to get it working properly and also I think the documentation is not that clear about what it calculates precisely, but when using the option "-geneList" it outputs what you want (% covered by 1/2/3/50/100/etc)
svl is offline   Reply With Quote
Old 07-10-2012, 04:16 AM   #3
Senior Member
Location: Germany

Join Date: Oct 2008
Posts: 401

Have a look at the samtools depth command too if you struggle with GATK.
colindaven is offline   Reply With Quote

genome coverage, ngs, reference genome

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 10:23 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO