Entering edit mode
2.9 years ago
Pierre Lindenbaum
164k
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
