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Old 04-28-2011, 04:38 PM   #1
jflores
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Location: Mexico

Join Date: Mar 2011
Posts: 7
Default Conversion from Complete Genomics Data to SAM/BAM

Hi There !

This thread is intended to questions related to conversion from Complete Genomics Data to SAM/BAM formats.

So here's mine:

I'm trying to get BAM files for some of the individuals sequenced by CG. I want all reads mapped to the reference and not just alignments around variants (evidenceDnbs files) so I downloaded all MAP data associated with the individuals of my interest and I got an structure data like this for each of the individuals:

i.e
NA06994
GS06994-1100-36-MAP
GS19360-FS3-L01
mapping_GS19360-FS3-L01_001.tsv.bz2
reads_GS19360-FS3-L01_001.tsv.bz2
..
reads_GS19360-FS3-L01_011.tsv.bz2
mapping_GS19360-FS3-L01_011.tsv.bz2
GS19360-FS3-L02
GS19360-FS3-L03
GS19360-FS3-L04
GS19360-FS3-L05
..
GS20181-FS3-L08

Theres no other way to get a BAM file for a particular location or chromosome (my interest) than going through the entire set of files. Im currently converting each of the reads and mapping files to BAM files (Its taking quite a long) using the map2sam command provided by CG here:

http://cgatools.sourceforge.net/docs...ls-methods.pdf

My question is: In order to get a full genome BAM file do I need to make first BAM files for all those reads/mapping pairs and them merge them all using samtools? I think the answer is yes you do but Im still a bit confused with this data structure and why there are so many folders and files for every single individual.

Many thanks in advance,
J. Rodrigo Flores
jflores@lcg.unam.mx
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Old 04-28-2011, 04:46 PM   #2
jason.laramie
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Location: Boston

Join Date: Feb 2011
Posts: 3
Default

Hi,
Yes that is correct. If you are interested in a particular region we have a program to do just that which is not part of cgatools. Please email me and I can send it to you.

jlaramie@completegenomics.com
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Old 04-28-2011, 05:01 PM   #3
jflores
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Location: Mexico

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Hi Jason,

Cheers for the response ! I'm interested just in one chromosome so I'm e-mailing you right now,
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Old 04-28-2011, 05:31 PM   #4
ECO
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Jflores,

Please don't repost all over the site again. Thanks!

Eric
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