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101 bytes added
, 15:11, 6 December 2014
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| It is usually useful to examine the call sets against known data sets for the passed variants. | | It is usually useful to examine the call sets against known data sets for the passed variants. |
| | | |
− | In order to do this, you need to update indel.reference.txt to point to the reference files.
| + | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
| + | If you are running outside the workshop, you will need to update indel.reference.txt to point to the reference files. |
| + | <div class="mw-collapsible-content"> |
| cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt | | cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt |
| | | |
| Edit indel.reference.txt and specify the correct path to ${SS} | | Edit indel.reference.txt and specify the correct path to ${SS} |
| nedit ${OUT}/indel.reference.txt | | nedit ${OUT}/indel.reference.txt |
− | *'''Replace all occurrences of <code>username</code> with your username (or the correct path to your seqshop example directory).''' | + | *'''Replace the path to the reference files with the path to your seqshop example directory.''' |
| *:[[File:IndelRef.png]] | | *:[[File:IndelRef.png]] |
| + | </div> |
| + | </div> |
| | | |
| ${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS" | | ${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS" |