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| | {{:GotCloud: Configuration}} | | {{:GotCloud: Configuration}} |
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| − | ====Additional User Config Files Settings====
| + | See [[#Variant Calling Command-line Options/Configuration Settings|Variant Calling Command-line Options/Configuration Settings]] for more information on Configuration options. |
| − | {| 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 !! Command-line Flag !! Value Description !! Default Value
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| − | |-
| |
| − | |CHRS||--chrs || pace separated list of chromosomes to process || 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X
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| − | |-
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| − | | BAM_LIST|| --list || path to the [[#BAM List File|BAM List File]] || $(OUT_DIR)/bam.list
| |
| − | |}
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| | | | |
| − | ====Targeted/Exome Sequencing Settings==== | + | ==== Example Configuration File ==== |
| − | If you are running Targeted/Exome Sequencing, the user should specify:
| |
| − | | |
| − | {| 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 !! Value Description
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| − | |-
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| − | |UNIFORM_TARGET_BED|| Bed file of targeted regions (same bed for all samples)
| |
| − | |-
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| − | |MULTIPLE_TARGET_MAP|| Filename of file mapping: sample id -> bed file of targeted regions
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| − | Each line of the file contains: [SM_ID] [TARGET_BED]
| |
| − | |-
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| − | |OFFSET_OFF_TARGET|| Number of bases by which to extend the target region
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| − | (default is 0, do not extend the target region)
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| − | |-
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| − | |SAMTOOLS_VIEW_TARGET_ONLY || '''true''': speeds up processing by excluding off-target regions initially when performing samtools view
| |
| − | | |
| − | '''false''' (default): off-target regions are not excluded when performing samtools view, but are excluded at a later step
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| − | | |
| − | '''Warning:''' You may not want to set this to true due to it may:
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| − | *''make command line too long''
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| − | *''produce an error if reads overlap multiple targeted regions''
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| − | ** see: [[GotCloud: FAQs#Targetted/Exome|GotCloud: FAQs->Targetted/Exome]]
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| − | |}
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| − | | |
| − | ==== Chromosome X Calling ====
| |
| − | For proper Chromosome X calling, it is recommended to specify a PED file with sex information:
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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 !! Value Description
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| − | |-
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| − | |PED_INDEX|| ped file containing sampleID (2nd column) and sex (5th column)
| |
| − | |}
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| − | | |
| − | Format of PED file:
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| − | :<code>familyID sampleID fatherID motherID sex</code>
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| − | * Only <code>sampleID</code> and <code>sex</code> are used
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| − | | |
| − | === Example Configuration File === | |
| | Example configuration file where reference files happen to be stored in /path/reference, and bam index file in path/freeze5 | | Example configuration file where reference files happen to be stored in /path/reference, and bam index file in path/freeze5 |
| | CHRS = 20 22 | | CHRS = 20 22 |
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| | HM3_VCF = $(REF_DIR)/hapmap3_r3_b37.sites.vcf.gz | | HM3_VCF = $(REF_DIR)/hapmap3_r3_b37.sites.vcf.gz |
| | DBSNP_VCF = $(REF_DIR)/dbsnp_135.b37.sites.vcf.gz | | DBSNP_VCF = $(REF_DIR)/dbsnp_135.b37.sites.vcf.gz |
| | + | |
| | + | |
| | + | == Variant Calling Command-line Options/Configuration Settings == |
| | + | {{:GotCloud: Variant Calling Options}} |
| | + | |
| | | | |
| | == Running == | | == Running == |
