rvtests
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zhanxw
rare variant analysis
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
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 [email protected] 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.
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
ParameterList Mon Mar 25 09:45:20 2019
--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.
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
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.