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4 bytes removed
, 14:24, 17 October 2014
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| # Look inside the output directory to see the new indel directories: | | # Look inside the output directory to see the new indel directories: |
| #:<pre>ls output</pre> | | #:<pre>ls output</pre> |
− | #:[[File:IndelSnpOutput.png.png|700px]] | + | #:[[File:IndelSnpOutput.png|900px]] |
| #:#<code>aux</code> - intermediate indel files | | #:#<code>aux</code> - intermediate indel files |
| #:#<code>final</code> - final output of Indel pipeline | | #:#<code>final</code> - final output of Indel pipeline |
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| # Important Indel output is in <code>output/final</code> | | # Important Indel output is in <code>output/final</code> |
| #:<pre> ls output/final/</pre> | | #:<pre> ls output/final/</pre> |
− | #: [[File:IndelFinal.png|700px]] | + | #: [[File:IndelFinal.png|900px]] |
| # Look at the final Indel VCF file. | | # Look at the final Indel VCF file. |
| #: <pre>zless output/final/all.genotypes.vcf.gz</pre> | | #: <pre>zless output/final/all.genotypes.vcf.gz</pre> |
− | #: Scroll down some: [[File::IndelLess.png|700px]] | + | #: Scroll down some: [[File::IndelLess.png|900px]] |
| ## Check that GotCloud found the expected Indel at 22:36662041 | | ## Check that GotCloud found the expected Indel at 22:36662041 |
| ##:<pre>tabix output/final/all.genotypes.vcf.gz 22:36662041-36662041|less -S</pre> | | ##:<pre>tabix output/final/all.genotypes.vcf.gz 22:36662041-36662041|less -S</pre> |
− | #:[[File::IndelTabix.png|700px]] | + | ##:[[File:IndelTabix.png|900px]] |
| | | |
| == Exit & Terminate == | | == Exit & Terminate == |
| # Exit from your terminal | | # Exit from your terminal |
| # Terminate your Amazon Instance | | # Terminate your Amazon Instance |