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.

  • By default, GotCloud looks for the reference/resource files in the gotcloud.ref subdirectory within the base GotCloud directory
  • To look in a different directory, set your reference/resource file location by setting either of the following to that path:
    • REF_DIR in your configuration file
    • --ref_dir on the command-line
Description Configuration Key Default Value Pipelines Special Info
Reference fasta REF $(REF_DIR)/human.g1k.v37.fa align, snpcall, indel Additional Files Required
DBSNP VCF File DBSNP_VCF $(REF_DIR)/dbsnp_135.b37.vcf.gz align, snpcall Must be tabixed
HapMap3 VCF File HM3_VCF $(REF_DIR)/hapmap_3.3.b37.sites.vcf.gz align, snpcall Must be tabixed
OMNI VCF File OMNI_VCF $(REF_DIR)/1000G_omni2.5.b37.sites.PASS.vcf.gz snpcall Must be tabixed
INDEL VCF File(s) INDEL_PREFIX $(REF_DIR)/1kg.pilot_release.merged.indels.sites.hg19 snpcall .chr#.vcf extension will be appended
INDEL_VCF alternate configuration setting if all INDEL sites are in a single VCF rather than broken up by chromosome Must be tabixed


Reference fasta Files

Reference Sequence in fasta format

  • Contains reference base at each reference position
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
    • Expected to be at the same location as the reference file
    • 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
align, snpcall, indel .fai bin/samtools faidx ref.fa
align, snpcall, indel -bs.umfa If it does not already exist, GotCloud automatically creates this file in same directory as the REF file
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

DBSNP VCF File

VCF file containing known dbsnp variant positions

  • Must be bgzip'd and tabix'd
Configuration Key Default Value
DBSNP_VCF $(REF_DIR)/dbsnp_142.b37.vcf.gz
Pipeline Use
align recalibration (exclude known dbsnps when generating recalibration tables) & qplot
snpcall generating filtered VCF summary statistics

HapMap3 VCF File

HapMap3 Polymorphic Sites VCF File

  • Must be bgzip'd and tabix'd
Configuration Key Default Value
HM3_VCF $(REF_DIR)/hapmap_3.3.b37.sites.vcf.gz
Pipeline Use
align verifyBamID (contamination checking)
snpcall generating filtered VCF summary statistics & positive example sites for SVM filtering

OMNI VCF File

VCF file containing OMNI positions

  • Must be bgzip'd and tabix'd
Configuration Key Default Value
OMNI_VCF $(REF_DIR)/1000G_omni2.5.b37.sites.PASS.vcf.gz
Pipeline Use
snpcall positive example sites for SVM filtering

INDEL VCF File(s)

VCF file containing known INDEL positions

Configuration Key Default Value
INDEL_PREFIX $(REF_DIR)/1kg.pilot_release.merged.indels.sites.hg19
INDEL_VCF alternate configuration setting if all INDEL sites are in a single VCF rather than broken up by chromosome
Pipeline Use
snpcall used to filter variants that are too close to a known indel
  • Use INDEL_PREFIX if path/ contains a separate file for each chromosome in the format: indels.sites.hg19.chr#.vcf for each # chromosome being processed
  • Use INDEL_VCF if you have all chromosomes in a single VCF file (it can be, but does not have to be a gz file)

Downloadable Reference and Resource Files

  • When running on Amazon, a default set of reference files are included in the GotCloud AMI in the default REF_DIR


Installing Genetic Reference and Resource Files

Choose a destination for these files and install them as shown below. We'll assume you will use gotcloud/gotcloud.ref. Replace gotcloud with the path to where you installed gotcloud. 

cd gotcloud   # path to where you installed gotcloud

If you use a path other than a gotcloud.ref subdirectory of gotcloud, note this path as you will need to set either of the following to the installation path:

  • REF_DIR in your configuration file
  • --ref_dir on the command-line


Get & Install the Resource Files

GotCloud 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.

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