SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
samtools mpileup multiple bam files lizzi Bioinformatics 9 03-09-2016 05:40 AM
Samtools mpileup calling independantly on multiple files rjohnp Bioinformatics 2 07-24-2013 07:31 AM
bowtie2: aligning multiple input files ksw9 Genomic Resequencing 2 05-13-2013 01:59 PM
[B]Mpileup on multiple BAM files, common SNPs?[/B] hbt Bioinformatics 4 02-05-2013 01:48 AM
MIRA3 multiple input files from same tech grassgirl Bioinformatics 6 11-10-2011 09:09 AM

Reply
 
Thread Tools
Old 11-19-2015, 03:07 AM   #1
Axel
Junior Member
 
Location: St Andrews

Join Date: Feb 2014
Posts: 8
Default mpileup and multiple input files

Hi All,

Is there any reason why the order in which .bam files are given to mpileup would affect the number of sites in the mpileup file?

I have 8 .bam files and I need to have an mpileup file with the samples in a particular order in the columns. I have run mpileup twice with the following settings:

Code:
samtools mpileup -d 1000000 -I -f in_genome.fasta 1st.bam 2nd.bam ... > out.mpileup
When I run it again with a different order of the input .bam files I get a massively different mpileup file that then affects how many SNPs are called/analysed downstream.

I am using samtools version 0.1.19
Axel is offline   Reply With Quote
Old 11-19-2015, 04:30 AM   #2
jkbonfield
Senior Member
 
Location: Cambridge, UK

Join Date: Jul 2008
Posts: 146
Default

I've no idea, but you should use samtools-1.2 as 0.1.19 is pretty ancient now.
jkbonfield is offline   Reply With Quote
Old 11-19-2015, 04:43 AM   #3
Axel
Junior Member
 
Location: St Andrews

Join Date: Feb 2014
Posts: 8
Default

Thanks jkbonfield. I'll try updating in case it's just a version issue. Still seems like odd behaviour though.
Axel is offline   Reply With Quote
Old 11-25-2015, 12:35 AM   #4
Axel
Junior Member
 
Location: St Andrews

Join Date: Feb 2014
Posts: 8
Default

I have now tried with the newer version of samtools (v. 1.2). This at least gives me mpileup files that are the same size. Hopefully this was just a weird version bug. We'll see what the downstream analyses turn up.
Axel is offline   Reply With Quote
Reply

Tags
multiple bam file, samtools, samtools mpileup

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 12:54 AM.


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