hope you are doing well, I just wanted to report an issue that the --min-callrate filter is not working at least for the skat-o test. I tried with and without this filter and got the same results however with RAREMETAL got different results. Afterward, I filtered my VCF using bcftools F_MISSING <=0.05 and then ran skat-o test with epacts and got the same results as for RAREMETAL with a call rate of 0.95. so I think the --min-callrate filter in EPACTS does not work.
I am using this version of EPACTS "e4dfca2d79a4c559e654d7bce52bc422b471f923"
Hi,
hope you are doing well, I just wanted to report an issue that the --min-callrate filter is not working at least for the skat-o test. I tried with and without this filter and got the same results however with RAREMETAL got different results. Afterward, I filtered my VCF using bcftools F_MISSING <=0.05 and then ran skat-o test with epacts and got the same results as for RAREMETAL with a call rate of 0.95. so I think the --min-callrate filter in EPACTS does not work.
I am using this version of EPACTS "e4dfca2d79a4c559e654d7bce52bc422b471f923"
Kind Regards, Haider