Extract Negative chromosome(gene) location from VCF files

I have about 3000 genes list and their chromosome locations(start and end). Some of the locations have negative positions as you can see below in the table. I think this mean these genes are position referenced from negative strand. I need to extract these genes from VCF file, but there aren't any negative location in VCF file. Can someone please explain me how this issue could be addressed when extracting these gene locations from VCF files.

   gene_id symbol chromosome start_location end_location
1  "1"     "A1BG" "19"       " -58858171"   " -58864865"
2  "10"    "NAT2" "8"        "  18248754"   "  18258723"
3  "100"   "ADA"  "20"       " -43248162"   " -43280376"
4  "1000"  "CDH2" "18"       " -25530926"   " -25616549"

vcf extract vcf chromosome location gene location

• 2,346 views • link

updated 10.3 years ago by Devon Ryan

• written 10.3 years ago by MAPK

1 answer

The negative positions are typically used to indicate the - strand. Yes this is incredibly unintuitive. So " -58858171" " -58864865" should be 58858171-58864865 on the - strand.

• 0 views • link

written 10.3 years ago by Devon Ryan