...
The best option is to use the ones in $BI if they are there (in $BI/ref_database/GATK) (NOTE: You can join the BioITeam and put them there!! Free storage this way!). Otherwise make your own local copy from those provided by GATK. TACC does not maintain these for the community (yet).
Expand title Tips on downloading, setting up GATK bundles... To pull GATK resource bundles and check them:
ftp ftp.broadinstitute.org
username: gsapubftp-anonymous<find bundle you want>
prompt
bin
mget *
Then: cd to dir, fix md5 files:
for file in `ls *.md5`; do sed -i 's/\(\/\).*\(\/\)//' $file; done
do md5 check:
for file in `ls *.md5`; do md5sum -c $file; done
- If you are in a non-model system, you are on your own to make the resource bundle. For instance, if you have a fasta file of your reference then you'll need to use the picard tool CreateSequenceDictionary.jar to make a dictionary of it for GATK. Use "module load picard" and then "ls $TACC_PICARD_DIR" to see all the picard tools at TACC.
...