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GotCloud: Genetic Reference and Resource Files (view source)

Revision as of 12:00, 14 May 2015

4,571 bytes added ,  12:00, 14 May 2015
→‎DBSNP VCF File
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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]].
 +
* By default, GotCloud looks for the reference/resource files in the <code>gotcloud.ref</code> subdirectory within the base GotCloud directory
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* To look in a different directory, set your reference/resource file location by setting either of the following to that path:
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** <code>REF_DIR</code> in your configuration file
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** <code>--ref_dir</code> on the command-line
    +
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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! Description !! Configuration Key !! Default Value !! Pipelines !! Special Info
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|-
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| [[#Reference fasta Files| Reference fasta]] || REF || $(REF_DIR)/human.g1k.v37.fa
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| align, snpcall, indel || [[#Additional files generated from the reference fasta|Additional Files Required]]
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|-
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| [[#DBSNP VCF File|DBSNP VCF File]] || DBSNP_VCF || $(REF_DIR)/dbsnp_135.b37.vcf.gz
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| align, snpcall || Must be tabixed
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|-
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| [[#HapMap3 VCF File|HapMap3 VCF File]] || HM3_VCF || $(REF_DIR)/hapmap_3.3.b37.sites.vcf.gz
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| align, snpcall || Must be tabixed
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|-
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| [[#OMNI VCF File|OMNI VCF File]] || OMNI_VCF || $(REF_DIR)/1000G_omni2.5.b37.sites.PASS.vcf.gz
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| snpcall || Must be tabixed
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|-
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| rowspan="2"|[[#INDEL VCF File(s)|INDEL VCF File(s)]] || INDEL_PREFIX || $(REF_DIR)/1kg.pilot_release.merged.indels.sites.hg19 || rowspan="2"|snpcall || .chr#.vcf extension will be appended
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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''||Must be tabixed
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|}
   −
=== Required Files ===
     −
==== Human Reference Files ====
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=== Reference fasta Files ===
 
Reference Sequence in fasta format
 
Reference Sequence in fasta format
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* Contains reference base at each reference position
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{| 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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! Pipeline !! Step !! Required Extensions !! Command to Create !! More Information
 
! Pipeline !! Step !! Required Extensions !! Command to Create !! More Information
 
|-
 
|-
−
| all || ||.fai || <code>bin/samtools faidx ref.fa</code>
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| align, snpcall, indel || ||.fai || <code>bin/samtools faidx ref.fa</code>
 
|-
 
|-
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| all || || -bs.umfa || automatically created in same directory as REF file by GotCloud
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| 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 || <code>bin/bwa index ref.fa</code> || http://bio-bwa.sourceforge.net/bwa.shtml  
 
| align || bwa mapping || .amb, .ann, .bwt, .pac, .sa || <code>bin/bwa index ref.fa</code> || http://bio-bwa.sourceforge.net/bwa.shtml  
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|}
 
|}
   −
==== DBSNP VCF File ====
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=== DBSNP VCF File ===
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VCF file containing known dbsnp variant positions
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* Must be bgzip'd and tabix'd
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{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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! Configuration Key !! Default Value
 +
|-
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| DBSNP_VCF || $(REF_DIR)/dbsnp_142.b37.vcf.gz
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|}
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{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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! Pipeline !! Use
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|-
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| align || recalibration (exclude known dbsnps when generating recalibration tables) & qplot
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|-
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| snpcall || generating filtered VCF summary statistics
 +
|}
   −
==== HapMap3 Polymorphic Sites VCF File ====
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=== HapMap3 VCF File ===
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HapMap3 Polymorphic Sites VCF File
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* Must be bgzip'd and tabix'd
   −
==== INDEL VCF File(s) ====
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{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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! Configuration Key !! Default Value
 +
|-
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| HM3_VCF || $(REF_DIR)/hapmap_3.3.b37.sites.vcf.gz
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|}
 +
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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! Pipeline !! Use
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|-
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| align || verifyBamID (contamination checking)
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|-
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| snpcall || generating filtered VCF summary statistics & positive example sites for SVM filtering
 +
|}
   −
==== OMNI VCF File ====
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=== OMNI VCF File ===
 +
VCF file containing OMNI positions
 +
* Must be bgzip'd and tabix'd
 +
 
 +
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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! Configuration Key !! Default Value
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|-
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| OMNI_VCF || $(REF_DIR)/1000G_omni2.5.b37.sites.PASS.vcf.gz
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|}
 +
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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! Pipeline !! Use
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|-
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| snpcall || positive example sites for SVM filtering
 +
|}
 +
 
 +
=== INDEL VCF File(s) ===
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VCF file containing known INDEL positions
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{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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! Configuration Key !! Default Value
 +
|-
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| INDEL_PREFIX || $(REF_DIR)/1kg.pilot_release.merged.indels.sites.hg19
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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''
 +
|}
 +
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
 +
! Pipeline !! Use
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|-
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| snpcall || used to filter variants that are too close to a known indel
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|}
 +
 
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* Use <code>INDEL_PREFIX</code> if <code>path/</code> contains a separate file for each chromosome in the format: <code>indels.sites.hg19.chr#.vcf</code> for each <code>#</code> chromosome being processed
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* Use <code>INDEL_VCF</code> 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 ==
 
== Downloadable Reference and Resource Files ==
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* When running on Amazon, a default set of reference files are included in the GotCloud AMI in the default <code>REF_DIR</code>
 +
    
'''Installing Genetic 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.
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Choose a destination for these files and install them as shown below.  We'll assume you will use '''gotcloud/gotcloud.ref'''.  Replace <code>gotcloud</code> with the path to where you installed gotcloud.
    
<code>
 
<code>
−
  <b>mkdir -p /usr/local/gotcloud.ref</b>   # Where you want the files installed
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  <b>cd gotcloud</b>   # path to where you installed gotcloud
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<b>cd /usr/local/gotcloud.ref</b>
   
</code>
 
</code>
   −
Note this path as you will need to set the variable '''REF_DIR''' in the configuration file for gotcloud.
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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:
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* <code>REF_DIR</code> in your configuration file
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* <code>--ref_dir</code> on the command-line
 +
 
    +
'''Get & Install the Resource Files'''
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'''Get the Resource Files'''
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GotCloud makes use of various reference and other genetic 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.
 
You are free to use your own files, of course, but we also are making the files we use available.
   −
<code>
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<ul>
−
#  The easiest way to get the data:
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<li> <div id="h37-db135">Human reference 37, dbsnp 135:</div></li>
 
  <b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db135-v3.tgz</b>
 
  <b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db135-v3.tgz</b>
−
  −
#  Another way:
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<b>ftp share.sph.umich.edu</b>
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Connected to share.sph.umich.edu.
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220 (vsFTPd 2.3.5)
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Name (share.sph.umich.edu:tpg): <b>anonymous</b>
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230 Login successful.
  −
Remote system type is UNIX.
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Using binary mode to transfer files.
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ftp> <b>prompt</b>
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Interactive mode off.
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ftp> <b>cd gotcloud</b>
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250 Directory successfully changed.
  −
ftp> <b>mget ref/h37-db135-v3.tgz</b>
  −
ftp> <b>quit</b>
  −
221 Goodbye.
  −
</code>
  −
  −
'''Install the Resource Files'''
  −
  −
<code>
   
  <b>tar xzf h37-db135-v3.tgz</b>
 
  <b>tar xzf h37-db135-v3.tgz</b>
 
  <b>rm -f h37-db135-v3.tgz</b>
 
  <b>rm -f h37-db135-v3.tgz</b>
−
</code>
+
<li><div id="h37-db142">Human reference 37, dbsnp 142:</div></li>
 +
<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db142-v1.tgz</b>
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<b>tar xzf h37-db142-v1.tgz</b>
 +
<b>rm -f h37-db142-v1.tgz</b>
 +
<li><div id="hs37d5-db142">Human reference 37 with decoy, dbsnp 142:</div></li>
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<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/hs37d5-db142-v1.tgz</b>
 +
<b>tar xzf hs37d5-db142-v1.tgz</b>
 +
<b>rm -f hs37d5-db142-v1.tgz</b>
 +
</ul>
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/11837...13224"

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