Open sbaheti opened 5 years ago
Can you verify that the variants of the gene exist in the vcf file?
Sent from my iPhone
On Mar 7, 2019, at 1:30 PM, sbaheti notifications@github.com wrote:
hi
I am having difficulties running the tool and get the output. The analysis skips all the variants for a gene and doesn't give out any results. Do you know what is wrong with the input ?
Thanks !
log file: [INFO] Program version: 20190205 [INFO] Git Version: c86e589 [INFO] Parameters BEGIN
ParameterList created by m078940 on mforgehn2.mayo.edu at Thu Mar 7 13:05:43 2019
--inVcf "/research/bsi/projects/PI/Rakela_Jorge_jxr14/secondary/s210022.ALF/variants/variants.vcf.gz" --out "/home/mayo/m078940/outRakela" --pheno "../../../covariate.file.tsv" --burden "cmc" --geneFile "/research/bsi/data/refdata/ensembl/human/gene/gtf/release-78/processed/2015_02_25/Homo_sapiens.GRCh38.78.mod.GGPS.refFlat" --gene "WASH7P" [INFO] Parameters END [INFO] Analysis started at: Thu Mar 7 13:05:43 2019 [INFO] Loaded [ 26 ] samples from genotype files [INFO] Loaded [ 26 ] sample phenotypes [INFO] Loaded 0 male, 0 female and 26 sex-unknown samples from ../../../covariate.file.tsv [INFO] Loaded 18 cases, 8 controls, and 0 missing phenotypes [WARN] -- Enabling binary phenotype mode -- [INFO] Analysis begins with [ 26 ] samples... [INFO] Loaded [ 1 ] genes. [INFO] Impute missing genotype to mean (by default) [INFO] Analysis started [INFO] Gene WASH7P has 0 variants, skipping [INFO] Analyzed [ 0 ] variants from [ 1 ] genes/regions [INFO] Analysis ends at: Thu Mar 7 13:05:44 2019 [INFO] Analysis took 1 seconds
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YES the variants exist, i also tried it without specifying any gene and in the log file it records all the genes are skipped as there are no variants. Not sure about the issue.
do you have any other suggestion i can try to make it work ?
i tried it again with a different statistics but still the same error to skip all the variants and this time i didn't specify any genes. Am i missing some parameter ?
[INFO] Program version: 20190205 [INFO] Git Version: c86e589efef15382603300dc7f4c3394c82d69b8 [INFO] Parameters BEGIN
--inVcf "variants.vcf.gz" --out "out9" --pheno "covariate.file.tsv" --burden "zeggini" --geneFile "Homo_sapiens.GRCh38.78.mod.GGPS.refFlat" [INFO] Parameters END [INFO] Analysis started at: Mon Mar 25 09:45:20 2019 [INFO] Loaded [ 26 ] samples from genotype files [INFO] Loaded [ 26 ] sample phenotypes [INFO] Loaded 0 male, 0 female and 26 sex-unknown samples from covariate.file.tsv [INFO] Loaded 18 cases, 8 controls, and 0 missing phenotypes [WARN] -- Enabling binary phenotype mode -- [INFO] Analysis begins with [ 26 ] samples... [INFO] Loaded [ 58157 ] genes. [INFO] Impute missing genotype to mean (by default) [INFO] Analysis started [INFO] Gene DDX11L1 has 0 variants, skipping [INFO] Gene WASH7P has 0 variants, skipping ......
Hello @zhanxw, I am getting exactly the same error as @sbaheti. Here is an example to reproduce the error:
refFlat.txt
SLMAP NM_007159 chr3 + 57757255 57930016 57757651 57927388 21 57757255,57831382,57841298,57847196,57849753,57857732,57858087,57860698,57861948,57864547,57871635,57890040,57896510,57896872,57907883,57909075,57912380,57913157,57916905,57922888,57927295, 57757849,57831530,57841371,57847233,57849816,57857828,57858159,57860839,57862086,57864716,57871698,57890100,57896591,57896932,57908006,57909150,57912701,57913275,57917077,57923023,57930016,
SLMAP NM_001304422 chr3 + 57889913 57930016 57896880 57927388 10 57889913,57896510,57896872,57907883,57909075,57912380,57913157,57916905,57922888,57927295, 57890100,57896591,57896932,57908006,57909150,57912701,57913275,57917077,57923023,57930016,
SLMAP NM_001304421 chr3 + 57757255 57930016 57757651 57927388 20 57757255,57831382,57841298,57847196,57849753,57857732,57858087,57860698,57861948,57864547,57890040,57896510,57896872,57907883,57909075,57912380,57913157,57916905,57922888,57927295, 57757849,57831530,57841371,57847233,57849816,57857828,57858159,57860839,57862086,57864716,57890100,57896591,57896932,57908006,57909150,57912701,57913275,57917077,57923023,57930016,
SLMAP NM_001304423 chr3 + 57889913 57930016 57896880 57927388 8 57889913,57896510,57896872,57912380,57913157,57916905,57922888,57927295, 57890100,57896591,57896932,57912701,57913275,57917077,57923023,57930016,
SLMAP NM_001304420 chr3 + 57757255 57930016 57757651 57927388 22 57757255,57831382,57841298,57847196,57849753,57857732,57858087,57860698,57861948,57864547,57864806,57871635,57890040,57896510,57896872,57907883,57909075,57912380,57913157,57916905,57922888,57927295, 57757849,57831530,57841371,57847233,57849816,57857828,57858159,57860839,57862086,57864716,57864857,57871698,57890100,57896591,57896932,57908006,57909150,57912701,57913275,57917077,57923023,57930016,
SLMAP NM_001311178 chr3 + 57889913 57930016 57896880 57925928 11 57889913,57896510,57896872,57907883,57909075,57912380,57913157,57916905,57922888,57925844,57927295, 57890100,57896591,57896932,57908006,57909150,57912701,57913275,57917077,57923023,57925934,57930016,
SLMAP NM_001311179 chr3 + 57889913 57918482 57896880 57917155 7 57889913,57896510,57896872,57909075,57912380,57913157,57916905, 57890100,57896591,57896932,57909150,57912701,57913275,57918482,
test.vcf.gz
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2 S3 S4 S5 S6 S7 S8 S9 S10 S11 S12
chr3 57757839 . A G 367.99 PASS AC=1;AF=0.042;AN=24;BaseQRankSum=-2.812;ClippingRankSum=0;DP=412;ExcessHet=3.0103;FS=4.01;InbreedingCoeff=-0.0435;MLEAC=1;MLEAF=0.042;MQ=60;MQRankSum=0;QD=17.52;ReadPosRankSum=-1.469 GT:AD:DP:GQ:PL 0/1:7,14:21:99:403,0,187 0/0:41,1:42:99:0,114,1465 0/0:38,0:38:99:0,102,1530 0/0:33,0:33:90:0,90,1350 0/0:33,0:33:81:0,81,1215 0/0:30,0:30:78:0,78,1170 0/0:42,0:42:99:0,120,1800 0/0:43,0:43:99:0,117,1755 0/0:29,0:29:81:0,81,1215 0/0:30,0:30:87:0,87,1305 0/0:37,0:37:99:0,105,1575 0/0:34,0:34:87:0,87,1305
chr3 57896989 rs762608342 A G 304.99 PASS AC=1;AF=0.042;AN=24;BaseQRankSum=-3.955;ClippingRankSum=0;DB;DP=433;ExcessHet=3.0103;FS=0;InbreedingCoeff=-0.0435;MLEAC=1;MLEAF=0.042;MQ=60;MQRankSum=0;QD=10.52;ReadPosRankSum=0.321 GT:AD:DP:GQ:PL 0/0:36,0:36:99:0,105,1575 0/0:42,0:42:99:0,117,1755 0/0:32,0:32:81:0,81,1215 0/0:43,0:43:99:0,120,1800 0/0:37,0:37:96:0,96,1440 0/0:37,0:37:99:0,108,1620 0/0:45,0:45:99:0,120,1800 0/0:24,0:24:66:0,66,990 0/1:19,14:33:99:332,0,594 0/0:52,0:52:99:0,120,1800 0/0:34,1:35:89:0,89,1237 0/0:41,0:41:99:0,111,1665
test.ped
fid iid father_id mother_id sex pheno
A S1 NA NA 1 2
A S2 NA NA 2 1
A S3 NA NA 1 1
A S4 NA NA 1 1
B S5 NA NA 1 1
B S6 NA NA 1 2
B S7 NA NA 2 1
C S8 NA NA 1 2
C S9 NA NA 2 1
C S10 NA NA 2 1
C S11 NA NA 2 2
C S12 NA NA 2 2
Command
/path/to/rvtests_v2.1.0/executable/rvtest --inVcf test.vcf.gz \
--pheno test.ped --pheno-name pheno \
--out results --geneFile refFlat.txt --burden cmc,cmcWald,zeggini,zegginiWald --vt price --kernel skat,kbac --gene SLMAP
RVTEST log
Retrieve remote version failed, use '--noweb' to skip.
[INFO] Program version: 20190205
[INFO] Analysis started at: Thu Apr 11 15:44:48 2019
[INFO] Loaded [ 12 ] samples from genotype files
[INFO] Loaded [ 12 ] sample phenotypes
[INFO] Loaded 6 male, 6 female and 0 sex-unknown samples from test.ped
[INFO] Loaded 5 cases, 7 controls, and 0 missing phenotypes
[WARN] -- Enabling binary phenotype mode --
[INFO] Analysis begins with [ 12 ] 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 [ 1 ] genes.
[INFO] Impute missing genotype to mean (by default)
[INFO] Analysis started
[INFO] Gene SLMAP has 0 variants, skipping
[INFO] Analyzed [ 0 ] variants from [ 1 ] genes/regions
[INFO] Analysis ends at: Thu Apr 11 15:44:48 2019
[INFO] Analysis took 0 seconds
RVTESTS finished successfully
Hello @zhanxw -- are there any updates on this error? I have the same issue and wasn't sure if it was ever resolved. thank you.
I am facing exactly the same issue. Does anyone have an advice?
https://github.com/zhanxw/rvtests/issues/80#issuecomment-482121514 https://github.com/matmu Did you manage to resolve this?
@ayub1985 found out that the program cannot handle vcf files properly if there is "chr" before the chromosome number for the variants.
Hi there,
I am having the same problem and I already deleted the "chr" part. Do you have any other sugestion?
Thank you in advance
Hi, I'm having the same problem.
Cross-posted on biostars: https://www.biostars.org/p/9504551/
edit: removing the chr prefix fixed the problem.
I have removed chr from refFlat file and from vcf but I am still getting 0 variants for all genes
You should remove the 'chr' from vcf files not the refFlat file.
Hi there,
I am having the same problem and I already deleted the "chr" part. Do you have any other sugestion?
Thank you in advance
You should remove the 'chr' from vcf files not the refFlat file.
hi
I am having difficulties running the tool and get the output. The analysis skips all the variants for a gene and doesn't give out any results. Do you know what is wrong with the input ?
Thanks !
log file: [INFO] Program version: 20190205 [INFO] Git Version: c86e589efef15382603300dc7f4c3394c82d69b8 [INFO] Parameters BEGIN
ParameterList created by m078940 on mforgehn2 at Thu Mar 7 13:05:43 2019
--inVcf "variants.vcf.gz" --out "out" --pheno "../../../covariate.file.tsv" --burden "cmc" --geneFile "Homo_sapiens.GRCh38.78.mod.GGPS.refFlat" --gene "WASH7P" [INFO] Parameters END [INFO] Analysis started at: Thu Mar 7 13:05:43 2019 [INFO] Loaded [ 26 ] samples from genotype files [INFO] Loaded [ 26 ] sample phenotypes [INFO] Loaded 0 male, 0 female and 26 sex-unknown samples from ../../../covariate.file.tsv [INFO] Loaded 18 cases, 8 controls, and 0 missing phenotypes [WARN] -- Enabling binary phenotype mode -- [INFO] Analysis begins with [ 26 ] samples... [INFO] Loaded [ 1 ] genes. [INFO] Impute missing genotype to mean (by default) [INFO] Analysis started [INFO] Gene WASH7P has 0 variants, skipping [INFO] Analyzed [ 0 ] variants from [ 1 ] genes/regions [INFO] Analysis ends at: Thu Mar 7 13:05:44 2019 [INFO] Analysis took 1 seconds