Re: [Bammds-users] bammds

[José Víctor Moreno Mayar]

Hey Niall, 

2 quick questions:

1. Are you using the HGDP reference panel we are distributing, or your own?

2. Could you try changing the header with samtools reheader? For the weird chromosomes (sex chrs, mt, random, un, etc) just leave them as they are. So the idea would be to just to remove "chr" from the autosomes. 

Cheers, 

Víctor

On Fri, Sep 26, 2014 at 9:09 AM, OSullivan Niall <address@hidden> wrote:

Hi Anna,
Thanks for getting back to me. I have attached the samheader in the txt file.  The first one is how my original sam file looked like . Then I used sed and grep  to change the samheaders and remove any unassigned chromosomes respectively. I have attached the samheader of the modified bam file in samheader2 text fille.

Best wishes

Niall

-----Original Message-----

From: Anna-Sapfo [mailto:address@hidden]
Sent: venerdì 26 settembre 2014 08.26
To: OSullivan Niall; address@hidden
Subject: Re: [Bammds-users] bammds

Hello Niall,
We would like to fix the bug so it works with your file as well.
Could you just copy paste the header of your bam file (samtools view -H)?

I will upload our reference to an ftp site for you but its a busy day so i dont know if i will get to it today.

Thanks!
anna

On 25-09-2014 17:18, OSullivan Niall wrote:
> I can't, the data is far too confidential to be circulated now.
>
> The genome was downloaded from here
> http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/
>
> Best
>
> Niall
>
> -----Original Message-----
> From: address@hidden [mailto:address@hidden] On Behalf Of
> Ole Tange
> Sent: giovedì 25 settembre 2014 16.48
> To: OSullivan Niall
> Cc: address@hidden
> Subject: Re: bammds
>
> On Thu, Sep 25, 2014 at 4:39 PM, OSullivan Niall <address@hidden> wrote:
>> Hi
>> 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 where?
> Can you give me access to all the data you used, so I can reproduce your problem? And a link to the HG19 file you used.
>
>
> /Ole

--

José Víctor Moreno Mayar
Centre for GeoGenetics
University of Copenhagen