Conversion from Complete Genomics Data to SAM/BAM

[jflores]

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

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

http://cgatools.sourceforge.net/docs/1.3.0/cgatools-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 I’m 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
[email protected]

[jason.laramie]

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.

[email protected]

[jflores]

Hi Jason,

Cheers for the response ! I'm interested just in one chromosome so I'm e-mailing you right now,

[ECO]

Jflores,

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

Eric