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Revision as of 21:28, 16 June 2014
, 21:28, 16 June 2014no edit summary
== Examining GotCloud Indel Input files ==
== Examining GotCloud Indel Input files ==
The GotCloud Indel caller takes the same inputs as GotCloud snpcall.
The GotCloud Indel caller takes the same inputs as GotCloud snpcall.
* BAMs->INDELs rather than BAMs->SNPs
If you want a reminder, of what they look like, here is a link to the previous tutorial : [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical#Examining_GotCloud_SnpCall_Input_files|GotCloud SnpCall Input Files]]
If you want a reminder, of what they look like, here is a link to the previous tutorial : [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical#Examining_GotCloud_SnpCall_Input_files|GotCloud SnpCall Input Files]]
== Running GotCloud Indel ==
== Running GotCloud Indel ==
${GC}/gotcloud indel --conf ${IN}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000
${GC}/gotcloud indel --conf ${IN}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000
* --numjobs tells GotCloud how many jobs to run in parallel
** Depends on your system
* --region 22:36000000-37000000
** The sample files are just a small region of chromosome 22, so to save time, we tell GotCloud to ignore the other regions
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Curious if it started running properly? Check out this screenshot:
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[[File:indelStart.png|550px]]
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This should take about 4-5 minutes to run.
* It should end with a line like: <code>Commands finished in 289 secs with no errors reported</code>
If you cancelled GotCloud part way through, just rerun your GotCloud command and it will pick up where it left off.
== Examining GotCloud indel Ouptut ==
Let's look at the output directory:
ls ${OUT}
;Do you see any new files or directories?
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* View Annotated Screenshot:
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[[File:indelOut.png|500px]]
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Let's look at the <code>final</code> directory:
ls ${OUT}/final
Just a <code>chr22</code> directory, so look inside of there:
ls ${OUT}/vcfs/chr22
;Can you identify the final indel VCF?
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* Answer & annotated directory listing:
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<ul>
<li>all.genotypes.vcf.gz</li>
</ul>
[[File:indelOutFinal.png|600px]]
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