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| | snpcall || Must be tabixed | | | 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 | + | | 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 |
| |- | | |- |
− | | INDEL_VCF || ''alternate configuration setting if all INDEL sites are in a single VCF rather than broken up by chromosome'' | + | | 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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| ! Configuration Key !! Default Value | | ! Configuration Key !! Default Value |
| |- | | |- |
− | | DBSNP_VCF || $(REF_DIR)/dbsnp_135.b37.vcf.gz | + | | DBSNP_VCF || $(REF_DIR)/dbsnp_142.b37.vcf.gz |
| |} | | |} |
| {| 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" |
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| === INDEL VCF File(s) === | | === INDEL VCF File(s) === |
| VCF file containing known INDEL positions | | VCF file containing known INDEL 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" | | {| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" |
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| | | |
| == Downloadable Reference and Resource Files == | | == Downloadable Reference and Resource Files == |
| + | * 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 '''gotcloud/gotcloud.ref'''. Replace <code>gotcloud</code> with the path to where you installed gotcloud. | | 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>cd gotcloud</b> # path to where you installed gotcloud | | <b>cd gotcloud</b> # path to where you installed gotcloud |
− | <b>mkdir -p gotcloud.ref</b>
| |
− | <b>cd gotcloud.ref</b>
| |
| </code> | | </code> |
| | | |
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| * <code>--ref_dir</code> on the command-line | | * <code>--ref_dir</code> on the command-line |
| | | |
− | '''Get the Resource Files''' | + | |
| + | '''Get & Install the Resource Files''' |
| + | |
| GotCloud makes use of various reference and other genetic 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. | | You are free to use your own files, of course, but we also are making the files we use available. |
| | | |
− | <code> | + | <ul> |
| + | <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> |
− | </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> |
| + | <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> |
| + | <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> |