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, 16:23, 15 June 2014
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| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
| <ul> | | <ul> |
− | <li><code>beagle</code> directory</li> : Beagle output | + | <li><code>beagle</code> directory : Beagle output</li> |
− | <li><code>thunder</code> directory</li> : Thunder output | + | <li><code>thunder</code> directory : Thunder output</li> |
| <li><code>umake.beagle.conf</code> : Configuration values used for GotCloud beagle</li> | | <li><code>umake.beagle.conf</code> : Configuration values used for GotCloud beagle</li> |
| <li><code>umake.beagle.Makefile</code> : GNU makefile for commands run as part of GotCloud beagle</li> | | <li><code>umake.beagle.Makefile</code> : GNU makefile for commands run as part of GotCloud beagle</li> |
| <li><code>umake.beagle.Makefile.log</code> : Log of the GotCloud beagle run</li> | | <li><code>umake.beagle.Makefile.log</code> : Log of the GotCloud beagle run</li> |
| <li><code>umake.thunder.*</code> files : Contain the configuration & steps used in GotCloud thunder</li> | | <li><code>umake.thunder.*</code> files : Contain the configuration & steps used in GotCloud thunder</li> |
| + | </ul> |
| + | </div> |
| + | </div> |
| + | </ul> |
| + | |
| + | Let's take a look at that interesting location we found in the [[SeqShop:_Sequence_Mapping_and_Assembly_Practical#Accessing_BAMs_by_Position|alignment tutorial]] : chromosome 22, positions 36907000-36907100 |
| + | |
| + | Use tabix to extract that from the VCFs: |
| + | ${GC}/bin/tabix ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz 22:36907000-36907100 |less -S |
| + | |
| + | ;Are there any variants in this region? |
| + | <ul> |
| + | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
| + | <li>Answer:</li> |
| + | <div class="mw-collapsible-content"> |
| + | <ul> |
| + | <li>Yes!</li> |
| + | <li>Positions:</li> |
| + | <ul> |
| + | <li><code>36907001</code>; Ref: T, Alt: C - that's what we saw before</li> |
| + | <li><code>36907098</code>; Ref: T, Alt: C - that's what we saw before</li> |
| + | </ul> |
| + | </ul> |
| + | </div> |
| + | </div> |
| + | </ul> |
| + | |
| + | ;What is HG00551's genotype at these positions? |
| + | #First check which sample number HG00551 is: |
| + | zcat ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz |grep "#CHROM" |
| + | * That will help you figure out it's genotype. |
| + | <ul> |
| + | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
| + | <li>Answer:</li> |
| + | <div class="mw-collapsible-content"> |
| + | <ul> |
| + | <li>It is the first sample</li> |
| + | <li><code>0|1</code>: Heterozygous</li> |
| + | <li><code>1|1</code>; Homozygous Alt (C)</li> |
| </ul> | | </ul> |
| </div> | | </div> |
| </div> | | </div> |
| </ul> | | </ul> |