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Jump to navigationJump to searchSeqShop: Variant Calling and Filtering for INDELs Practical, June 2014 (view source)
Revision as of 10:59, 11 July 2014
, 10:59, 11 July 2014→Comparison with other data sets
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 /home/mktrost/ with the path to your seqshop directory.'''
*'''Replace all occurrences of <code>username</code> with your username (or the correct path to your seqshop example directory).'''
*:[[File:IndelRef.png]]
${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"
