Question: Convert COSMIC VCF coordinates to that of ensembl format?
0
gravatar for simplitia
27 days ago by
simplitia40
simplitia40 wrote:

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
ADD COMMENTlink written 27 days ago by simplitia40
1

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

It looks like you have what you need already

ADD REPLYlink written 27 days ago by RamRS30k
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