How to filter structural variants in a vcf file on size

Question

[Abdel]

I have a vcf file with structural variants (mainly deletions), and I want to filter out only deletions with a specific size (>10kb for example) and write those deletions to a separate vcf file. How can I do this?

Answer 1

[Ashutosh Pandey]

Similar question answered already here: Filtering Gatk Indel Output Length 20+

[Abdel]

Thank you very much!

Answer 2

[victorrg]

Hi! I just was looking for this, and since is the top result in google search I found it useful to answer with the current GATK version (4.2.6.1).

What worked for me is this commands:

gatk SelectVariants \
     -V input.vcf \
     --select-type-to-include DEL \
     --min-indel-size 10000 \
     -O output.vcf

Those, and more, arguments can be found in: https://gatk.broadinstitute.org/hc/en-us/articles/5358856605339-SelectVariants#--variant

I used the docker image for GATK. I think it works fine and saves a lot of time, this is the tutorial I followed: https://gatk.broadinstitute.org/hc/en-us/articles/360035889991--How-to-Run-GATK-in-a-Docker-container#article-comments

Quick disclaimer: I'm new to bioinformatics so maybe there is some other way to do this filter using other tools, but I found GATK to be the most easy and straightforward.

Hope it helps!