Tools for rare variant burden analysis

Question

[quentin54520]

Hello,

I would like to be able to see if within my patient cohort there are genes that are enriched in potentially pathogenic variants compared to what is in gnomad. unfortunately the only tools I managed to find use the old version of the reference genome (hg19) while all my data was generated on grch38, so I would like to know if anyone knows a tool that works with grch38 . As a last resort I will do a liftover of my vcf to hg19 but I don't know how reliable it is and the number of variations I risk losing.

Thanks you in advance.

[Pierre Lindenbaum]

so I would like to know if anyone knows a tool that works with grch38

http://zhanxw.github.io/rvtests/ ?