Re: [Bammds-users] bammds

[Anna-Sapfo]

Hello Niall,
Here is the reference genome we have been using:
ftp://ftp_20140819_4291:address@hidden
We are expecting the chromosomes to appear in the same order in the genotype file as in the bamfile.
for the genotype file it seems very standard to have chromosomes: 1-22, X,Y, MT
Yet yours seem to appear in this order:
1-7, X, 8-20, Y, 19, 22, 21, MT
this is likely to create issues for you with other tools.
so its i not the "chr"  issue but it is likely the order of the chromosomes.
We will try to adapt the error message so  that its easier to understand.
If you attempt a remapping: can you let us know if it works?
Thanks!
anna

On 09/26/2014 09:09 AM, OSullivan Niall 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