SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Samtools-mpileup aslihan Bioinformatics 3 01-18-2017 11:53 PM
samtools mpileup using -l or -r vplagnol Genomic Resequencing 3 05-08-2013 11:23 PM
mpileup consensus behaviour rwness Bioinformatics 5 07-24-2012 08:12 AM
samtools mpileup Ling1 Bioinformatics 1 05-24-2012 11:09 AM
strange bwa/samtools behaviour (?) francesconea Bioinformatics 0 04-12-2011 06:15 AM

Reply
 
Thread Tools
Old 02-03-2011, 09:55 AM   #1
CHRYSES
Member
 
Location: Netherlands

Join Date: Dec 2009
Posts: 13
Default samtools mpileup unexpected behaviour

Hi,

The command below:
samtools mpileup -ugf 454AllContigs.fasta my.bam | bcftools view -bvcg - > var.raw.bcf


exits with the following error:

[mpileup] 2 samples in 1 input files
<mpileup> Set max per-sample depth to 4000
[bcf_sync] incorrect number of fields (7 != 5) at 43:101



Would that mean that the bam file is missing fields? It is created via the standard methods as outlined in the BWA and samtools manuals.

The alignments are made using bwa bwasw where 454 reads served as query and references.

The RG fields are created according to the samtools manual.

The following fields have been set while merging:
@RG ID:dUMMY1 SM:dUMMY1 LB:454 PL:454
@RG ID:dUMMY2 SM:dUMMY2 LB:454 PL:454
(...)


Does anyone have an idea what the error cause is? If so, please share it here.


The description 7 != 5 is not helping much to track the reason.

Thanks,

Best regards
CHRYSES is offline   Reply With Quote
Old 02-03-2011, 05:12 PM   #2
lh3
Senior Member
 
Location: Boston

Join Date: Feb 2008
Posts: 693
Default

This has not happened for a while. Could you try the latest version from SVN? What if you use "mpileup -I" to disable indel calling. If both fail, do you have a small example for me to try? Thanks.
lh3 is offline   Reply With Quote
Old 02-04-2011, 01:35 AM   #3
CHRYSES
Member
 
Location: Netherlands

Join Date: Dec 2009
Posts: 13
Default

Quote:
Originally Posted by lh3 View Post
This has not happened for a while. Could you try the latest version from SVN? What if you use "mpileup -I" to disable indel calling. If both fail, do you have a small example for me to try? Thanks.
The proposed solution with "mpileup -I" has indeed avoided the crash+error, but at the same time it renders samtools to a snp caller only. No indels are called.

I had done an svn checkout of the trunk lately. The version I am using is:

$ svn info
Path: .
URL: https://samtools.svn.sourceforge.net...samtools/trunk
Repository Root: https://samtools.svn.sourceforge.net/svnroot/samtools
Repository UUID: fd675618-d7d1-4fc3-a54f-e58cce934862
Revision: 902
Node Kind: directory
Schedule: normal
Last Changed Author: lh3lh3
Last Changed Rev: 902
Last Changed Date: 2011-01-24 03:46:18 +0100 (Mon, 24 Jan 2011)


The samtools binary shows this:
$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.12-10 (r896)


Note that I could not use GATK for indel calling in 454 reads so I wanted to give samtools a shot in this, but it seems like it cannot handle it (yet).

Do you have any suggestions on making the samtools work with this kind of data?

Thanks.

Regards
CHRYSES is offline   Reply With Quote
Old 03-08-2011, 06:56 AM   #4
Seq84
Member
 
Location: Italy

Join Date: Feb 2011
Posts: 19
Default

Quote:
The proposed solution with "mpileup -I" has indeed avoided the crash+error, but at the same time it renders samtools to a snp caller only. No indels are called.
Me too i had the same problem of CHRYSES and i've solved with -I option.

Why it happens? is a version problem (0.1.12-10 (r896-r862)) or is a problem internal to the .bam file?

Thanks in advance
Seq84 is offline   Reply With Quote
Old 06-19-2012, 07:19 AM   #5
cnoirot
Junior Member
 
Location: Toulouse, France

Join Date: Feb 2012
Posts: 3
Default

I still have a problem with the version 0.1.18 (r982:295)
The reference base is always set to N but in fasta file it's not the case !
I can't perform varFilter.
Do you have ever seen this problem ?
cnoirot is offline   Reply With Quote
Reply

Tags
error, mpileup, samtools, snp

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 06:28 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO