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vatlab / varianttools

software tool for the manipulation, annotation, selection, and analysis of variants in the context of next-gen sequencing analysis
https://vatlab.github.io/vat-docs/
GNU General Public License v3.0
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All association tests have failed (Association tests on 324063 groups have completed. 324063 failed) #151

Open marionamujal opened 3 years ago

marionamujal commented 3 years ago

Hello, I am requesting for your help on this. I am running a common variant association analysis with variant tools using docker. However, all the association tests are failing. I wonder what could be the cause. Any assistance on this will be very much appreciated!

INFO: 314 samples are found
INFO: Grouping variants by 'variant.chr:variant.pos', please be patient ...
INFO: 324063 groups are found
WARNING: Temp files are not regenerated!
Testing for association: 100% [==========================================================================] 324,063/324,025 31.7/s in 02:50:36
WARNING: Field sample_size_SNV_permute has all missing values
WARNING: No valid integer values has been found for field sample_size_SNV_permute
WARNING: Field num_variants_SNV_permute has all missing values
WARNING: No valid integer values has been found for field num_variants_SNV_permute
WARNING: Field total_mac_SNV_permute has all missing values
WARNING: No valid integer values has been found for field total_mac_SNV_permute
WARNING: Field beta_x_SNV_permute has all missing values
WARNING: No valid float values has been found for field beta_x_SNV_permute
WARNING: Field pvalue_SNV_permute has all missing values
WARNING: No valid float values has been found for field pvalue_SNV_permute
WARNING: Field std_error_SNV_permute has all missing values
WARNING: No valid float values has been found for field std_error_SNV_permute
WARNING: Field num_permutations_SNV_permute has all missing values
WARNING: No valid integer values has been found for field num_permutations_SNV_permute
**INFO: Association tests on 324063 groups have completed. 324063 failed.**
INFO: Indexing linked field variant.chr, variant.pos
INFO: Using annotation DB common_variants as common_variants in project Variant_association_tools_001.
INFO: Annotation database used to record results of association tests. Created on Thu, 05 Nov 2020 21:58:50
INFO: 324063 out of 3006180 variant.chr, variant.pos are annotated through annotation database common_variants
BoPeng commented 3 years ago

Could you at least send the exact command that you have used? There could be many reasons and it is difficult for me to diagnose without a test project.

karthickji commented 1 year ago

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">

##fileformat=VCFv4.1 |   |   |   |   |   |   |   |   |   |   -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- ##fileDate=20130319 |   |   |   |   |   |   |   |   |   |   ##source=GenerateReportDataAndVCFv2.2.2.0 |   |   |   |   |   |   |   |   |   |   ##reference=HumanNCBI37_UCSC |   |   |   |   |   |   |   |   |   |   ##phasing=none |   |   |   |   |   |   |   |   |   |   ##INFO= |   |   |   |   |   |   |   |   |   |   ##INFO= |   |   |   |   |   |   |   |   |   |   ##INFO= |   |   |   |   |   |   |   |   |   |   ##INFO= |   |   |   |   |   |   |   |   |   |   ##INFO= |   |   |   |   |   |   |   |   |   |   ##FILTER= |   |   |   |   |   |   |   |   |   |   ##FORMAT= |   |   |   |   |   |   |   |   |   |   ##FORMAT= |   |   |   |   |   |   |   |   |   |   #CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | FORMAT | 12AD50320_MAXGT | 12AD50320_POLY chr16 | 60054 | rs62028702 | A | C | 23 | PASS | DP=9 | GT:GQ | 0/1:23 | 0/1:56 chr16 | 60087 | rs62028703 | C | G | 27 | PASS | DP=13 | GT:GQ | 0/1:27 | 0/1:60 chr16 | 60095 | rs62028704 | G | T | 26 | PASS | DP=13 | GT:GQ | 0/1:26 | 0/1:59 chr16 | 60120 | . | G | A | 11 | q20 | DP=10 | GT:GQ | 1/0:11 | 1/0:43

this is my vcf file i don't understand MAXGT and POLY. how to remove MAXGT AND POLY, i am go to gwas study but thia MAXGT AND POLY was my problem . pls any one help me