Hi,

this is the first time I'm using rvtests https://github.com/zhanxw/rvtests (version: 20190205, git: c86e589efef15382603300dc7f4c3394c82d69b8)

the log file (including the command line) is:

Effective Options
    --inVcf indexed.vcf.gz
    --out prefix
    --pheno input.ped
    --burden cmc
    --vt price
    --kernel skat,kbac
    --kinship rel.kinship
    --geneFile genes.txt

[INFO]  Program version: 20190205
[INFO]  Analysis started at: Wed Jan  5 19:08:22 2022
[INFO]  Loaded [ 1249 ] samples from genotype files
[INFO]  Loaded [ 1249 ] sample phenotypes
[INFO]  Loaded 0 male, 0 female and 1249 sex-unknown samples from input.ped
[INFO]  Loaded 179 cases, 1070 controls, and 0 missing phenotypes
[WARN]  -- Enabling binary phenotype mode -- 
[INFO]  Analysis begins with [ 1249 ] samples...
[INFO]  Price's VT test significance will be evaluated using 10000 permutations at alpha = 0.05
[INFO]  SKAT test significance will be evaluated using 10000 permutations at alpha = 0.05 weight = Beta[beta1 = 1.00, beta2 = 25.00]
[INFO]  KBAC test significance will be evaluated using 10000 permutations at alpha = 0.05
[INFO]  Loaded [ 41 ] genes.
[INFO]  Family-based model not specified. Options related to kinship will be ignored here.
[INFO]  Impute missing genotype to mean (by default)
[INFO]  Analysis started

and then all the genes have no variants

[INFO]  Gene KCNIP1 has 0 variants, skipping
[INFO]  Gene NHP2 has 0 variants, skipping
[INFO]  Gene SAR1B has 0 variants, skipping
[INFO]  Gene PAIP2 has 0 variants, skipping
[INFO]  Gene CSNK1G3 has 0 variants, skipping

while there is clearly a variant for example for KCNIP1

$ bcftools view -G  indexed.vcf.gz | bcftools annotate -x '^INFO/ANN,INFO/AC' | grep KCNIP1 -m1
chr5    169780927   .   C   T   662.9   PASS    AC=1;ANN=T|missense_variant|MODERATE|KCNIP1|ENSG00000182132|transcript|ENST00000377360|protein_coding|1/8|c.47C>T|p.Ala16Val|437/1197|47/678|16/225||,T|missense_variant|MODERATE|KCNIP1|ENSG00000182132|transcript|ENST00000517344|nonsense_mediated_decay|1/4|c.47C>T|p.Ala16Val|235/639|47/129|16/42||

and the genes file use the same chromosome notation.

$ grep -m1 KCNIP1 genes.txt

KCNIP1  NM_001034838    chr5    +   169780880   170163636   169780880   170162810   8   169780880,170145761,170147324,170148836,170149716,170159803,170160839,170162762,    169780968,170145886,170147394,170148907,170149824,170159908,170160902,170163636,

what I'm I doing wrong ?

edit: related ? https://github.com/zhanxw/rvtests/issues/80