inquiry related to rsid

Question

[rheab1230]

Hello everyone,

I have .vcf files. I have remove indels and now have only SNP. I want to update id column in .vcf file with that of rsid in dbSNP since predixcan software require .vcf files to have rsid.

Is there any software which can update the information.

I am using dbSNP142.

Answer 1

[WouterDeCoster]

you can do that with vcfanno, and a TOML configuration file like the one below:

[[annotation]]
file="dbsnp.vcf.gz"
fields = ["ID"]
ops=["self"]
names=["rsid"]

[[postannotation]]
name="ID"
fields=["rsid"]
op="setid"
type="String"

[rheab1230]

okay, I will do that. Thank You