From Genome Analysis Wiki
Jump to navigationJump to search
91 bytes added
, 10:35, 11 July 2014
Line 319: |
Line 319: |
| 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.''' |
| + | |
| | | |
| ${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" |