GotCloud: Genetic Reference and Resource Files

Genetic Reference and Resource Files

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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.fa with the path/name of the reference fasta file

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. QPLOT: InputFiles

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