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Re: [Bammds-users] bammds

From: OSullivan Niall
Subject: Re: [Bammds-users] bammds
Date: Thu, 25 Sep 2014 14:39:56 +0000

I think it may be the reference file that was used for the bwa mapping. I used 
HG19 and I downloaded it directly from UCSC. You used a different one, but from 

Best wishes

-----Original Message-----
From: address@hidden [mailto:address@hidden On Behalf Of Ole Tange
Sent: mercoledì 24 settembre 2014 16.12
To: address@hidden
Cc: OSullivan Niall
Subject: Fwd: bammds

From Niall's description alone I cannot solve this.

I believe we support standard BAM, so my initial guess is that Niall's file is 
somehow non-standard and thus I would require an example file to see what goes 

Can anyone else pitch in?


---------- Forwarded message ----------
From: OSullivan Niall <address@hidden>
Date: Wed, Sep 24, 2014 at 11:33 AM
Subject: bammds
To: "address@hidden" <address@hidden>

Dear Ole Tange,

I am trying to use your bammds program to make a PCA plot of two merged shotgun 
programs. It asks me to change the notation and order of the chromosomes. I 
have tried to change the notation and order, but it results in the same error 
message. I would like to enquire if you have a script or method for converting 
bam files from the standard format to the one that is compatible with your 
program. I have searched online and been unable to find a solution.

Best regards



Niall O’Sullivan, BA, MSc


EURAC research

Institute for Mummies and the Iceman

Piazza Angela Nikoletti 14, I-39100

Bolzano, Italy

Tel: +39 0471 055 560

Fax: +39 0471 055 579

Email: address@hidden

PhD candidate

School of Archaeology

University College Dublin


Dublin 4, Ireland

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