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inquiry related to rsid

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.

twas vcf rsid predixcan
• 1,391 views • link
updated by Ram Ram • written by rheab1230 • rheab1230

1 answer

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"
• 0 views • link
written by WouterDeCoster WouterDeCoster

okay, I will do that. Thank You

• 0 views • link
written by rheab1230 • rheab1230

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