GotCloud: Genetic Reference and Resource Files

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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

DBSNP VCF File

Downloadable Reference and Resource Files

Installing Genetic Reference and Resource Files


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:
cd /tmp
wget ftp://share.sph.umich.edu/gotcloud/h37-db135.tgz

#  Another way:
cd /tmp
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 h37-db135.tar.gz
ftp> quit
221 Goodbye.

Install the Resource Files

Choose a destination for these files and install them as shown below (we'll assume you will use /usr/local/gotcloud.ref). 

mkdir -p /usr/local/gotcloud.ref    # Where you want the files installed
cd /usr/local/gotcloud.ref
tar xzf h37-db135.tar.gz
rm -f h37-db135.tar.gz

Note this path as you will need to set the variable REF_DIR in the configuration file for gotcloud.

Using Your own Reference Files

Human Reference

Generating BWA Reference Files

Use "bwa index" to generate the human reference files with the required extensions:

  • .amb
  • .ann
  • .bwt
  • .fai
  • .pac
  • .rbwt
  • .rpac
  • .rsa
  • .sa

See http://bio-bwa.sourceforge.net/bwa.shtml for more information about using "bwa index".

Generating GC Content File

The GC Content file is used by QPLOT. It is assumed to be at the same location as the reference file.

If the reference file is at path/ref.fa, the GC Content file is expected to be:path/ref.winsize100.gc


To generate the GC content file, run qplot: 

GOTCLOUD_DIR/bin/qplot --reference reference.fa --winsize windowSize
  • Replace reference.fa with the name of your human reference fasta file.
  • Replace windowSize with your desired window size, or leave out --winsize to use the default (100).

NOTE: You will get an 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.

But it was successful as long as you see (where reference is the name of your reference file): 

GC content file [ reference.winsize100.gc ] created.


See http://genome.sph.umich.edu/wiki/QPLOT#Input_files for more information.

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