Mercurial > repos > saskia-hiltemann > virtual_normal_analysis
comparison vcf2lv.sh @ 2:885ba15c2564 draft
Uploaded
| author | saskia-hiltemann |
|---|---|
| date | Mon, 03 Aug 2015 05:45:16 -0400 |
| parents | 1209f18a5a83 |
| children | 58815aed4ec3 |
comparison
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| 1:1c6710924e80 | 2:885ba15c2564 |
|---|---|
| 17 FS="\t"; | 17 FS="\t"; |
| 18 OFS="\t"; | 18 OFS="\t"; |
| 19 count=0; | 19 count=0; |
| 20 | 20 |
| 21 #output new header | 21 #output new header |
| 22 print "variantId", "chromosome", "begin", "end", "varType", "reference", "alleleSeq", "xRef" | 22 print "variantId", "chromosome", "begin", "end", "varType", "reference", "alleleSeq" |
| 23 }{ | 23 }{ |
| 24 | 24 |
| 25 if(substr($0,1,1)!="#" && $5 != "."){ #skip header or nonvariant entries (period in ALT column) | 25 if(substr($0,1,1)!="#" && $5 != "."){ #skip header or nonvariant entries (period in ALT column) |
| 26 | 26 |
| 27 # detect multivariants | 27 # detect multivariants |
| 83 alleleSeq=alt | 83 alleleSeq=alt |
| 84 } | 84 } |
| 85 | 85 |
| 86 #print output variant(s) | 86 #print output variant(s) |
| 87 | 87 |
| 88 if(chromosome != "chrM") | 88 print count, chromosome, start, end, varType, reference, alleleSeq |
| 89 print count, chromosome, start, end, varType, reference, alleleSeq, "" | |
| 90 | 89 |
| 91 count+=1 | 90 count+=1 |
| 92 } | 91 } |
| 93 } | 92 } |
| 94 }END{}' $vcffile > $outputfile | 93 }END{}' $vcffile > $outputfile |