Difference between revisions of "GotCloud: Genetic Reference and Resource Files"
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Revision as of 12:49, 23 October 2014
Genetic Reference and Resource Files
Back to parent: GotCloud
In order to run GotCloud, you need to provide Genetic Reference and Resource Files.
You can generate your own files or use the set available for download.
Required Files
Human Reference Files
Reference Sequence in fasta format
| Configuration Key | Default Value |
|---|---|
| REF | $(REF_DIR)/human.g1k.v37.fa |
| Pipeline | Use |
|---|---|
| align | mapping to reference, recalibration, quality control |
| snpcall | pileup & identify variants, summarize filtered variants |
| indel | discovery, genotyping |
Additional files generated from the reference fasta
In addition to the fasta file a few additional files generated from the fasta are required
- Already included with default reference files
- If you are using your own reference files, you will need to be sure to create these files
- Be sure to create these additional files using the version of tool being run by GotCloud (by default they are in the
gotcloud/bin/directory) - In the commands below, replace
ref.fawith the path/name of the reference fasta file
- Be sure to create these additional files using the version of tool being run by GotCloud (by default they are in the
| Pipeline | Step | Required Extensions | Command to Create | More Information |
|---|---|---|---|---|
| all | .fai | bin/samtools faidx ref.fa
| ||
| all | -bs.umfa | automatically created in same directory as REF file by GotCloud | ||
| align | bwa mapping | .amb, .ann, .bwt, .pac, .sa | bin/bwa index ref.fa |
http://bio-bwa.sourceforge.net/bwa.shtml |
| align | qplot | .winsize100.gc | bin/qplot --reference ref.fa |
NOTE: Ignore the error at the end of qplot that says:
FATAL ERROR - No SAM/BAM files provided, stopped! This error is due to using qplot to just generate a GC Content file and not also process a BAM file. |
DBSNP VCF File
HapMap3 Polymorphic Sites VCF File
INDEL VCF File(s)
OMNI VCF File
Downloadable Reference and Resource Files
Installing Genetic Reference and Resource Files Choose a destination for these files and install them as shown below. We'll assume you will use /usr/local/gotcloud.ref. If you use a different directory, replace /usr/local/gotcloud.ref with your path.
mkdir -p /usr/local/gotcloud.ref # Where you want the files installed
cd /usr/local/gotcloud.ref
Note this path as you will need to set the variable REF_DIR in the configuration file for gotcloud.
Get the Resource Files
The GotCloud Aligner and Umake makes use of various reference and other genetic resource files.
You are free to use your own files, of course, but we also are making the files we use available.
# The easiest way to get the data:
wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db135-v3.tgz
# Another way:
ftp share.sph.umich.edu
Connected to share.sph.umich.edu.
220 (vsFTPd 2.3.5)
Name (share.sph.umich.edu:tpg): anonymous
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> prompt
Interactive mode off.
ftp> cd gotcloud
250 Directory successfully changed.
ftp> mget ref/h37-db135-v3.tgz
ftp> quit
221 Goodbye.
Install the Resource Files
tar xzf h37-db135-v3.tgz
rm -f h37-db135-v3.tgz
