Merging consecutive non-variant calls

Question

[gmcinnes]

I'm looking for a tool that can merge non-variant segments from GATK together. Essentially what I'm looking for is the opposite of gvcftools' break_blocks command. Anyone know of anything?

Answer 1

[Chris Saunders]

It has not been maintained for current GATK, but this tool is designed to merge any non-variants from GATK 1.x all-sites output:

https://sites.google.com/site/gvcftools/home/configuration-and-analysis/gatk_to_gvcf-usage

[gmcinnes]

Thanks, Chris. What if I already have gvcfs with non-variant blocks, but want to use less stringent criteria to merge the non-variant blocks together?

[Chris Saunders]

Sorry, don't know of anything that would do this right out of the box..