Entering edit mode
4.1 years ago
simplitia
▴
130
HI so I downloaded the mutation VCF from COSMIC recently and realized that the coordinates are ones without the "chr" prefix so I'm wondering there are any tools to convert this coodinate sys to one without the chr prefix ( I believe this is the ensemble one).
I can use awk to replace and add +1, but on other threads I heard this is not a good idea.
thanks in advance.
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##source=COSMICv92
##reference=GRCh38
##INFO=<ID=OLD_VARIANT,Number=.,Type=String,Description="Original chr:pos:ref:alt encoding">
#CHROM POS ID REF ALT QUAL FILTER INFO
1 65797 COSV58737189 T C . . GENE=OR4F5_ENST00000641515;STRAND=+;LEGACY_ID=COSN23957695;SNP;CDS=c.9+224T>C;AA=p.?;HGVSC=ENST00000641515.2:c.9+224T>C;HGVSG=1:g.65797T>C;CNT=1
1 66041 COSV58737025 A G . . GENE=OR4F5_ENST00000641515;STRAND=+;LEGACY_ID=COSN24406961;CDS=c.9+468A>G;AA=p.?;HGVSC=ENST00000641515.2:c.9+468A>G;HGVSG=1:g.66041A>G;CNT=1
It looks like you have what you need already