http://genome.sph.umich.edu/w/index.php?title=GotCloud:_Reference_Files&feed=atom&action=historyGotCloud: Reference Files - Revision history2024-03-29T14:44:08ZRevision history for this page on the wikiMediaWiki 1.35.9http://genome.sph.umich.edu/w/index.php?title=GotCloud:_Reference_Files&diff=11690&oldid=prevMktrost: /* GotCloud Reference Files */2014-10-06T17:19:34Z<p><span dir="auto"><span class="autocomment">GotCloud Reference Files</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:19, 6 October 2014</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The chromosome 20 reference files required for the tutorial are included with the tutorial example data in $GCDATA/chr20Ref/. </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The chromosome 20 reference files required for the tutorial are included with the tutorial example data in $GCDATA/chr20Ref/. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>If you are running more than just chromosome 20, you will need whole genome reference files which can be downloaded from [[<del class="diffchange diffchange-inline">GotCloudReference</del>]].</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>If you are running more than just chromosome 20, you will need whole genome reference files which can be downloaded from [[<ins class="diffchange diffchange-inline">GotCloud: Genetic Reference and Resource Files</ins>]].</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
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<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">TODO</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>If you are using these reference files, you will only need to specify REF_DIR in your configuration file to the full path to where they are installed.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>If you are using these reference files, you will only need to specify REF_DIR in your configuration file to the full path to where they are installed.</div></td></tr>
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<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">TODO, maybe only provide info on how to use the DEFAULT reference.</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Move detailed description to generic gotcloud documentation. This is too much info for the Tutorial page!!!!</del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Genome sequence reference file'''</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Genome sequence reference file'''</div></td></tr>
</table>Mktrosthttp://genome.sph.umich.edu/w/index.php?title=GotCloud:_Reference_Files&diff=6654&oldid=prevMktrost: Created page with '= GotCloud Reference Files = Reference files are required for running both the alignment and variant calling pipelines. * Genome sequence reference files (needed for both pipel…'2013-03-05T23:41:12Z<p>Created page with '= GotCloud Reference Files = Reference files are required for running both the alignment and variant calling pipelines. * Genome sequence reference files (needed for both pipel…'</p>
<p><b>New page</b></p><div>= GotCloud Reference Files =<br />
Reference files are required for running both the alignment and variant calling pipelines. <br />
* Genome sequence reference files (needed for both pipelines)<br />
* DBSNP site VCF file (needed for both pipelines)<br />
* HAPMAP site VCF file (needed for both pipelines)<br />
* Indel sites file (need for variant calling pipeline)<br />
<br />
The chromosome 20 reference files required for the tutorial are included with the tutorial example data in $GCDATA/chr20Ref/. <br />
<br />
If you are running more than just chromosome 20, you will need whole genome reference files which can be downloaded from [[GotCloudReference]].<br />
<br />
TODO<br />
If you are using these reference files, you will only need to specify REF_DIR in your configuration file to the full path to where they are installed.<br />
<br />
<br />
<br />
<br />
TODO, maybe only provide info on how to use the DEFAULT reference.<br />
Move detailed description to generic gotcloud documentation. This is too much info for the Tutorial page!!!!<br />
<br />
'''Genome sequence reference file'''<br />
* FA_REF in the configuration file<br />
* human_g1k_v37_chr20* files in the Tutorial<br />
* Specify with a .fa or .fa.gz extension<br />
* Implies the existence of the following files at the same path, with the same name with the following extensions appended:<br />
** .fai<br />
*** fasta index file<br />
** .amb, .ann, .bwt, .pac, .rbwt, .rpac, .rsa, .sa<br />
*** for the BWA step of the alignment pipeline<br />
*** can be generated using TBD<br />
** .Gccontent<br />
*** for the QPLOT step of the alignment pipeline<br />
*** can be generated using TBD<br />
* Implies the existence of the following files with the same basename, but different extension:<br />
** .dict<br />
*** can be generated using TBD<br />
** -bs.umfa<br />
*** can be generated using TBD<br />
<br />
'''DBSNP site VCF file'''<br />
* DBSNP_VCF in the configuration file<br />
* dbsnp135_chr20.vcf.gz* in the Tutorial<br />
* Specify with a .vcf.gz extension<br />
* Implies the existence of .vcf.gz.tbi, the vcf index file<br />
<br />
'''HapMap site VCF file'''<br />
* HM3_VCF in the configuration file<br />
* hapmap_3.3.b37.sites.chr20.vcf.gz * in the Tutorial<br />
* Specify with a .vcf.gz extension<br />
* Implies the existence of .vcf.gz.tbi, the vcf index file<br />
<br />
'''Indel Sites VCF file'''<br />
* INDEL_PREFIX in the configuration file<br />
* 1kg.pilot_release.merged.indels.sites.hg19 in the Tutorial<br />
* Prefix, so excludes the extension but implies the existence of .chrXX.vcf.gz for each chromosome<br />
<br />
<br />
Below is the list of chromosome 20 reference files required for the tutorial and included with the tutorial example data in $GCDATA/chr20Ref/:<br />
<pre><br />
1kg.pilot_release.merged.indels.sites.hg19.chr20.vcf <br />
dbsnp135_chr20.vcf.gz <br />
dbsnp135_chr20.vcf.gz.tbi <br />
hapmap_3.3.b37.sites.chr20.vcf.gz <br />
hapmap_3.3.b37.sites.chr20.vcf.gz.tbi <br />
human_g1k_v37_chr20-bs.umfa <br />
human_g1k_v37_chr20.dict <br />
human_g1k_v37_chr20.fa <br />
human_g1k_v37_chr20.fa.amb <br />
human_g1k_v37_chr20.fa.ann <br />
human_g1k_v37_chr20.fa.bwt <br />
human_g1k_v37_chr20.fa.fai <br />
human_g1k_v37_chr20.fa.GCcontent <br />
human_g1k_v37_chr20.fa.pac <br />
human_g1k_v37_chr20.fa.rbwt <br />
human_g1k_v37_chr20.fa.rpac <br />
human_g1k_v37_chr20.fa.rsa <br />
human_g1k_v37_chr20.fa.sa <br />
</pre></div>Mktrost