http://genome.sph.umich.edu/w/index.php?action=history&feed=atom&title=GBR60vc.conf 2026-09-27T02:07:02Z Revision history for this page on the wiki MediaWiki 1.43.1 http://genome.sph.umich.edu/w/index.php?title=GBR60vc.conf&diff=6524&oldid=prev 2013-02-25T06:05:30Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <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 02:05, 25 February 2013</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l20">Line 20:</td> <td colspan="2" class="diff-lineno">Line 20:</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>* CHRS - this specifies which chromosomes to process</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>* CHRS - this specifies which chromosomes to process</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;"><div>** Leave this out of your configuration file if you want to process all chromosomes (1-22, X, Y)</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>** Leave this out of your configuration file if you want to process all chromosomes (1-22, X, Y)</div></td></tr> <tr><td class="diff-marker" data-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>* [[BAM_INDEX]] - file containing the samples &amp; BAMs to be processed</div></td><td class="diff-marker" data-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>* [[<ins style="font-weight: bold; text-decoration: none;">#GBR60bam.index|</ins>BAM_INDEX]] - file containing the samples &amp; BAMs to be processed</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;"><div>* Reference Information:</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>* Reference Information:</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;"><div>** AS - assembly value to put in the BAM</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>** AS - assembly value to put in the BAM</div></td></tr> </table>

Mktrost http://genome.sph.umich.edu/w/index.php?title=GBR60vc.conf&diff=6523&oldid=prev 2013-02-25T06:04:52Z

<p><span class="autocomment">GBR60bam.index</span></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <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 02:04, 25 February 2013</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l38">Line 38:</td> <td colspan="2" class="diff-lineno">Line 38:</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>It is recommended that you use absolute paths.  (This example does not use absolute paths in order to be flexible to where the data is installed, but using relative paths require it to be run from the correct directory.)</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>It is recommended that you use absolute paths.  (This example does not use absolute paths in order to be flexible to where the data is installed, but using relative paths require it to be run from the correct directory.)</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;"><br></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;"><br></td></tr> <tr><td class="diff-marker" data-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>GBR60bam.index<del style="font-weight: bold; text-decoration: none;">]] </del>=</div></td><td class="diff-marker" data-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>= GBR60bam.index =</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;"><div>The index file contains at least 3 tab-separated columns</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 index file contains at least 3 tab-separated columns</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;"><div># Sample name</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># Sample name</div></td></tr> </table>

Mktrost http://genome.sph.umich.edu/w/index.php?title=GBR60vc.conf&diff=6522&oldid=prev 2013-02-25T06:04:29Z

<p>Created page with &#039;=GBR60vc.conf= This is the configuration file for the variant calling pipeline in the <a href="/wiki/Tutorial:_GotCloud" title="Tutorial: GotCloud">GotCloud Tutorial</a> The configuration file contains KEY = VALUE settin…&#039;</p> <p><b>New page</b></p><div>=GBR60vc.conf=<br /> This is the configuration file for the variant calling pipeline in the [[Tutorial: GotCloud|GotCloud Tutorial]]<br /> <br /> The configuration file contains KEY = VALUE settings that override defaults and set specific values for the given run.<br /> <br /> &lt;pre&gt;<br /> CHRS = 20<br /> BAM_INDEX = GBR60bam.index<br /> ############<br /> # References<br /> REF_ROOT = chr20Ref<br /> #<br /> REF = $(REF_ROOT)/human_g1k_v37_chr20.fa<br /> INDEL_PREFIX = $(REF_ROOT)/1kg.pilot_release.merged.indels.sites.hg19<br /> DBSNP_VCF = $(REF_ROOT)/dbsnp135_chr20.vcf.gz<br /> HM3_VCF = $(REF_ROOT)/hapmap_3.3.b37.sites.chr20.vcf.gz<br /> &lt;/pre&gt;<br /> <br /> This configuration file sets:<br /> * CHRS - this specifies which chromosomes to process<br /> ** Leave this out of your configuration file if you want to process all chromosomes (1-22, X, Y)<br /> * [[BAM_INDEX]] - file containing the samples &amp; BAMs to be processed<br /> * Reference Information:<br /> ** AS - assembly value to put in the BAM<br /> ** FA_REF - the reference file (.fa extension), the additional files should be at the same location:<br /> *** human_g1k_v37_chr20-bs.umfa<br /> *** human_g1k_v37_chr20.fa<br /> *** human_g1k_v37_chr20.fa.fai<br /> ** INDEL_PREFIX - indel information<br /> ** DBSNP_VCF - a vcf containing the dbsnp positions<br /> ** HM3_VCF - hapmap vcf<br /> <br /> <br /> For running your own test, update the INDEX_FILE to point to your index file and the reference values to point to your references.<br /> <br /> This example uses reference files that are chr20 only in order to speed processing of the tutorial data. If you are using the default references, you may just need to update REF_DIR to the directory where they are installed. Full Reference files can be downloaded from [[GotCloudReference]].<br /> <br /> It is recommended that you use absolute paths. (This example does not use absolute paths in order to be flexible to where the data is installed, but using relative paths require it to be run from the correct directory.)<br /> <br /> = [[GBR60bam.index]] =<br /> The index file contains at least 3 tab-separated columns<br /> # Sample name<br /> # Population<br /> #* can be a comma separated list of populations<br /> #* specify ALL if you don&#039;t know the population or if you aren&#039;t interested in population specific information<br /> # BAM file name<br /> <br /> If you have more than one BAM file for each sample, separate them by tabs.<br /> <br /> <br /> &lt;pre&gt;<br /> HG00096 GBR bams/HG00096.bam<br /> HG00100 GBR bams/HG00100.bam<br /> HG00103 GBR bams/HG00103.bam<br /> HG00106 GBR bams/HG00106.bam<br /> HG00108 GBR bams/HG00108.bam<br /> HG00111 GBR bams/HG00111.bam<br /> HG00112 GBR bams/HG00112.bam<br /> HG00114 GBR bams/HG00114.bam<br /> HG00115 GBR bams/HG00115.bam<br /> HG00116 GBR bams/HG00116.bam<br /> HG00117 GBR bams/HG00117.bam<br /> HG00118 GBR bams/HG00118.bam<br /> HG00119 GBR bams/HG00119.bam<br /> HG00120 GBR bams/HG00120.bam<br /> HG00122 GBR bams/HG00122.bam<br /> HG00123 GBR bams/HG00123.bam<br /> HG00124 GBR bams/HG00124.bam<br /> HG00125 GBR bams/HG00125.bam<br /> HG00126 GBR bams/HG00126.bam<br /> HG00127 GBR bams/HG00127.bam<br /> HG00131 GBR bams/HG00131.bam<br /> HG00133 GBR bams/HG00133.bam<br /> HG00136 GBR bams/HG00136.bam<br /> HG00137 GBR bams/HG00137.bam<br /> HG00138 GBR bams/HG00138.bam<br /> HG00139 GBR bams/HG00139.bam<br /> HG00140 GBR bams/HG00140.bam<br /> HG00141 GBR bams/HG00141.bam<br /> HG00142 GBR bams/HG00142.bam<br /> HG00143 GBR bams/HG00143.bam<br /> HG00145 GBR bams/HG00145.bam<br /> HG00146 GBR bams/HG00146.bam<br /> HG00148 GBR bams/HG00148.bam<br /> HG00149 GBR bams/HG00149.bam<br /> HG00150 GBR bams/HG00150.bam<br /> HG00151 GBR bams/HG00151.bam<br /> HG00152 GBR bams/HG00152.bam<br /> HG00154 GBR bams/HG00154.bam<br /> HG00155 GBR bams/HG00155.bam<br /> HG00156 GBR bams/HG00156.bam<br /> HG00157 GBR bams/HG00157.bam<br /> HG00158 GBR bams/HG00158.bam<br /> HG00159 GBR bams/HG00159.bam<br /> HG00160 GBR bams/HG00160.bam<br /> HG00231 GBR bams/HG00231.bam<br /> HG00232 GBR bams/HG00232.bam<br /> HG00233 GBR bams/HG00233.bam<br /> HG00239 GBR bams/HG00239.bam<br /> HG00242 GBR bams/HG00242.bam<br /> HG00243 GBR bams/HG00243.bam<br /> HG00244 GBR bams/HG00244.bam<br /> HG00245 GBR bams/HG00245.bam<br /> HG00246 GBR bams/HG00246.bam<br /> HG00247 GBR bams/HG00247.bam<br /> HG00249 GBR bams/HG00249.bam<br /> HG00250 GBR bams/HG00250.bam<br /> HG00251 GBR bams/HG00251.bam<br /> HG00252 GBR bams/HG00252.bam<br /> HG00253 GBR bams/HG00253.bam<br /> HG00254 GBR bams/HG00254.bam<br /> &lt;/pre&gt;<br /> <br /> This example uses relative paths, but for greatest flexibility, absolute paths are recommended.</div>

Mktrost