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GotCloud: Genetic Reference and Resource Files (view source)

Revision as of 13:46, 23 October 2014

3,565 bytes added ,  13:46, 23 October 2014
→‎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]].
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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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! 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 || 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''
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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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|}
 
|}
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===== Additional files generated from the reference fasta =====
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==== 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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|}
 
|}
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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 gzip'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_135.b37.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 || recalibration (exclude known dbsnps when generating recalibration tables) & qplot
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|-
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| snpcall || generating filtered VCF summary statistics
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|}
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=== HapMap3 VCF File ===
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HapMap3 Polymorphic Sites VCF File
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* Must be gzip'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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| HM3_VCF || $(REF_DIR)/hapmap_3.3.b37.sites.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 || verifyBamID (contamination checking)
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|-
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| snpcall || generating filtered VCF summary statistics & positive example sites for SVM filtering
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|}
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=== OMNI VCF File ===
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VCF file containing OMNI positions
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* Must be gzip'd and tabix'd
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==== HapMap3 Polymorphic Sites VCF File ====
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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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|-
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| OMNI_VCF || $(REF_DIR)/1000G_omni2.5.b37.sites.PASS.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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| snpcall || positive example sites for SVM filtering
 +
|}
   −
==== INDEL VCF File(s) ====
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=== INDEL VCF File(s) ===
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VCF file containing OMNI positions
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* Must be gzip'd and tabix'd
   −
==== OMNI VCF File ====
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{| 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"
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! Pipeline !! Use
 +
|-
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| snpcall || positive example sites for SVM filtering
 +
|}
    
== Downloadable Reference and Resource Files ==
 
== Downloadable Reference and Resource Files ==
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/11838"

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