SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
samtools mpileup generates an empty output david.tamborero Bioinformatics 7 07-10-2020 06:55 AM
Unrecognized characters in the read base column of mpileup output charlie_sequencing Bioinformatics 1 11-06-2013 06:33 PM
Odd behavior using samtools mpileup, bcftools JimC Bioinformatics 7 05-21-2013 11:34 AM
Unstable output from mpileup/samtools KNS Bioinformatics 14 10-25-2011 01:38 AM
pysam IteratorSNPCall output different than the samtools mpileup aggp11 Genomic Resequencing 0 07-13-2011 10:25 AM

Reply
 
Thread Tools
Old 08-26-2011, 04:33 PM   #1
Bueller_007
Member
 
Location: Earth

Join Date: May 2010
Posts: 16
Default Odd characters in samtools mpileup output

I'm struggling to figure out what some of the characters in my samtools mpileup output are. Here's one of the offending bases (scaffold1:25513). There are many.

Code:
scaffold1       25513   G       20      <<,,,,,a,A,aa,a,AA..    #A.CCFG6G6F67E:F<6GF
So it tells me that the read depth is 20, and this is confirmed by counting the number of characters in each of the last two columns. But I have absolutely no idea what the "<" character represents in the read_bases column (column #5).

The only special characters I'm expecting to see are '.' and ',' (indicating forward and reverse matches) '+' and '-' (indicating indels), and '^' (followed by a symbol indicating read-mapping quality) and '$' (indicating the beginning and end of a read respectively).

So can anyone tell me what '<' means in column 5?


EDIT: To answer my own question somewhat, '<' and '>' indicate a "reference skip" according to the mpileup documentation. (Although they are not mentioned in the pileup format documentation, which is why I couldn't find them.) However, I have absolutely no idea what "reference skip" means, so I'm still out of luck. If it's referring to a base that is not covered (e.g. due to splicing) then shouldn't the coverage ideally be reported as 18, not 20?

Last edited by Bueller_007; 08-26-2011 at 04:52 PM.
Bueller_007 is offline   Reply With Quote
Reply

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 08:42 AM.


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