Annotating indels and SNVs
1
0
Entering edit mode
9 weeks ago
am29 ▴ 30

I have a vcf and bed file with around 17 million SNPs, indels, and SNVs. SNPs are annotated and have rsID, however, indels and SNVs don't have ID and appear as '.' I need all of them for my analyses, therefore I can't exclude any.

Is there any way to annotate indels and SNVs in a way to make them have provisional rsIDs? I already managed to rename bed file to contain something like baseposition_refallele_alt_allele as a variant ID, however, the software I am using (BFMAP, SLEMM) recognizes only rsIDs.

What can I do?

annotation indels SNV • 305 views
ADD COMMENT
2
Entering edit mode
9 weeks ago
gunzip -c in.vcf.gz | awk -F '\t' '/^#/ {print;next;} {OFS="\t";$3=sprintf("rs%d",NR);print;}'
ADD COMMENT
0
Entering edit mode

Thank you Pierre! It works!

ADD REPLY

Login before adding your answer.

Traffic: 2536 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6