Difference between revisions of "GotCloud: Genetic Reference and Resource Files"

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You can generate your own files or use the set available for [[#Downloadable Reference and Resource Files|download]].
 
You can generate your own files or use the set available for [[#Downloadable Reference and Resource Files|download]].
  
 +
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
 +
! Description !! Configuration Key !! Default Value !! Pipelines !! Special Info
 +
|-
 +
| [[#Reference fasta Files| Reference fasta]] || REF || $(REF_DIR)/human.g1k.v37.fa
 +
| align, snpcall, indel || [[#Additional files generated from the reference fasta|Additional Files Required]]
 +
|-
 +
| [[#DBSNP VCF File|DBSNP VCF File]] || DBSNP_VCF || $(REF_DIR)/dbsnp_135.b37.vcf.gz
 +
| align, snpcall || Must be tabixed
 +
|-
 +
| [[#HapMap3 VCF File|HapMap3 VCF File]] || HM3_VCF || $(REF_DIR)/hapmap_3.3.b37.sites.vcf.gz
 +
| align, snpcall || Must be tabixed
 +
|-
 +
| [[#OMNI VCF File|OMNI VCF File]] || OMNI_VCF || $(REF_DIR)/1000G_omni2.5.b37.sites.PASS.vcf.gz
 +
| snpcall || Must be tabixed
 +
|-
 +
| rowspan="2"|[[#INDEL VCF File(s)|INDEL VCF File(s)]] || INDEL_PREFIX || $(REF_DIR)/1kg.pilot_release.merged.indels.sites.hg19 || rowspan="2"|snpcall || rowspan="2"|Must be tabixed
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|-
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| INDEL_VCF || ''alternate configuration setting if all INDEL sites are in a single VCF rather than broken up by chromosome''
 +
|}
  
−
=== Required Files ===
 
  
−
==== Human Reference Files ====
+
=== Reference fasta Files ===
 
Reference Sequence in fasta format
 
Reference Sequence in fasta format
 +
* Contains reference base at each reference position
 +
 
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
 
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
 
! Configuration Key !! Default Value
 
! Configuration Key !! Default Value
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|}
 
|}
  
−
===== Additional files generated from the reference fasta =====
+
==== Additional files generated from the reference fasta ====
 
In addition to the fasta file a few additional files generated from the fasta are required
 
In addition to the fasta file a few additional files generated from the fasta are required
 
* Already included with default reference files
 
* Already included with default reference files
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|}
 
|}
  
−
==== DBSNP VCF File ====
+
=== DBSNP VCF File ===
 +
VCF file containing known dbsnp variant positions
 +
* Must be gzip'd and tabix'd
 +
 
 +
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
 +
! Configuration Key !! Default Value
 +
|-
 +
| DBSNP_VCF || $(REF_DIR)/dbsnp_135.b37.vcf.gz
 +
|}
 +
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
 +
! 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 gzip'd and tabix'd
 +
 
 +
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
 +
! Configuration Key !! Default Value
 +
|-
 +
| HM3_VCF || $(REF_DIR)/hapmap_3.3.b37.sites.vcf.gz
 +
|}
 +
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
 +
! 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 gzip'd and tabix'd
  
−
==== HapMap3 Polymorphic Sites VCF File ====
+
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
 +
! Configuration Key !! Default Value
 +
|-
 +
| OMNI_VCF || $(REF_DIR)/1000G_omni2.5.b37.sites.PASS.vcf.gz
 +
|}
 +
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
 +
! Pipeline !! Use
 +
|-
 +
| snpcall || positive example sites for SVM filtering
 +
|}
  
−
==== INDEL VCF File(s) ====
+
=== INDEL VCF File(s) ===
 +
VCF file containing OMNI positions
 +
* Must be gzip'd and tabix'd
  
−
==== OMNI VCF File ====
+
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
 +
! 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''
 +
|}
 +
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
 +
! Pipeline !! Use
 +
|-
 +
| snpcall || positive example sites for SVM filtering
 +
|}
  
 
== Downloadable Reference and Resource Files ==
 
== Downloadable Reference and Resource Files ==

Revision as of 13:46, 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.

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 Must be tabixed
INDEL_VCF alternate configuration setting if all INDEL sites are in a single VCF rather than broken up by chromosome


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
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

DBSNP VCF File

VCF file containing known dbsnp variant positions

  • Must be gzip'd and tabix'd
Configuration Key Default Value
DBSNP_VCF $(REF_DIR)/dbsnp_135.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 gzip'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 gzip'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 OMNI positions

  • Must be gzip'd and tabix'd
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 positive example sites for SVM filtering

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

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