Hello Geert,
For the best results, especially for SNPs, you will want to map directly
to the target genome. The genome Galaxy is using is the same primary
human genome the GATK team also uses - the 1000 genomes build 37 ->
"hg_g1k_v37". Click on the GATK links from one of the tools to see the
details. GATK provides liftOver files between the the genomes, and you
could install and use these with the liftOver tool, but not for BAM
datasets. Inputs are BED, Interval, GFF. (BAM -> SAM -> interval).
GATK also provides indexes (lifted) for hg19, but Galaxy does not
provide an hg19 genome that is sorted appropriately for GATK, or at
least not yet. RNA-seq tools and most other tools up until now required
sorting in one way, and now GATK requires sorting in another, but
keeping the database dbkey the same is important for visualization and
other functions. It can get complicated when moving between tools in a
history. We will likely have some 'best practice' solutions soon, but
for now, use the 1000 genomes build to keep it all simple:
Human (Homo sapients) (b37): hg_g1k_v37
The good news is that installing this genome has been greatly
simplified. The genome and indexes are now available on an rsync server.
You can simply download and add the genome directory and all the
contents. You will still need to create the .loc file entries but the
rest is done.
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
The "dbkey" is "hg_g1k_v37"
Hopefully one of the options works out for you!
Jen
Galaxy team
ps: You post ended up threading behind another post. I am not sure if
this was because you started with a reply, but changed the subject line?
This is not enough to start a new thread. Instead, please create a brand
new message in your email client, then copy over the mailing list email
address, add a subject line, and this will start a new thread that will
get tracked and not missed. Thanks!
On 8/15/12 1:16 AM, Geert Vandeweyer wrote:
Hi all,
We have recieved some bam files that were aligned to hg18. What would be
the easiest workflow to get a VCF file from GATK in build hg19 ? We are
running a local galaxy with only hg19 for the moment. Lifting the bam
file would be my first choice, providing support to hg18 by generating
all indices would be my last :-)
Best regards,
Geert
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
