Question: Expand annotation on a vcf file
0
gravatar for Dee
2.8 years ago by
Dee0
Dee0 wrote:

Hello!

I have a vcf file created by a bam file and another vcf file downloaded from ClinVar with all known variants with clinical significance. I have found the overlapping regions and I want to expand the annotation of the first file with the information from the second file (but I want to keep all the non pathological variants as well). Is there a function for this?

Thank you so much!

variantannotation vcf • 446 views
ADD COMMENTlink modified 2.8 years ago by Michael Lawrence10k • written 2.8 years ago by Dee0
Answer: Expand annotation on a vcf file
1
gravatar for Michael Lawrence
2.8 years ago by
United States
Michael Lawrence10k wrote:

Lets say you have two VRanges x and y from readVcfAsVRanges(). Then, in the devel version of Bioconductor (3.4), you can do:

merge(x, y, all.x=TRUE)

There is no need to find overlaps upfront. The two variant sets will be matched by position and alt.

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Michael Lawrence10k

That was so easy!

You saved the day!

Thank you so much!

ADD REPLYlink written 2.8 years ago by Dee0
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