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Contents is a small tools written in Python script to check input VCF files before association tests. It will report monomorphic sites, sites with reference alleles inconsistent with the reference genome, sites with invalid genotypes, non-snp site (e.g. indels), and all sites with allele frequencies greater than 0.5. After you passed the checking, you can go on to run rvtests - rare-variant test software.


Download from this and unzip downloaded file. This includes script, reference genome in FASTA format and its index file.


python -r hs37d5.fa -o test $your_VCF


Console output and .log file

Upon successfully running on the example file, you will obtain following information: -- check validity of VCF file for meta-analysis
version 1.3 (20130223)
contact or for problems.
Python version is [ ] 
Begin checking vcfFile [ example.vcf.gz ]
---------------     REPORT     ---------------
Total [ 18 ] lines processed
Examine [ 7 ] VCF header lines, [ 11 ] variant sites, [ 6 ] samples
[ 0 ] duplicated sites
[ 0 ] NonSNP site are outputted to [ tmp.check.nonSnp ]
[ 10 ] Inconsistent reference sites are outputted to [ tmp.check.ref ]
[ 0 ] Variant sites with invalid genotypes are outputted to [ tmp.check.geno ]
[ 1 ] Alternative allele frequency > 0.5 sites are outputted to [ ]
[ 1 ] Monomorphic sites are outputted to [ tmp.check.mono ]
---------------     ACTION ITEM     ---------------
* Read tmp.check.ref, for autosomal sites, make sure the you are using the forward strand
* Upload these files to the ftp: tmp.check.log tmp.check.dup tmp.check.noSnp tmp.check.ref tmp.check.geno tmp.check.mono

.check.nonSnp file

This file includes all non-SNP sites. These can be detected when the length of your reference allele or alternative allele is larger than one. For example, reference allele is AT. Non-SNP sites also includes reference alleles that are not composited from 'A', 'C', 'G', 'T' alleles or alternative alleles that are not composited from 'A', 'T', 'G', 'C', '.' alleles.

.check.ref file

This file includes the variant sites that do not match reference alleles. That can happen when: (1) variant chromosome names do not appear in the reference genome file. You will see a line with "FailedGetBase" and chromosome:position from the input VCF file; (2) reference alleles do not match. You will see "MismatchRefBase" and chromosome:position:trueReferenceAllele-referenceAlleleInVCF:referenceAlleleInVCF. For example:

MismatchRefBase 19:50578409:G-C/T
FailedGetBase   23:208316

.check.geno file

This file contains the line number in which genotypes are not found or not formatted correctly. You will get "IndividualMissingGTField" and "IndividualHasInvalidGT" warnings. file

This file contains the sites where alternative allele frequency larger than 0.5 . It is normal that this files contains a number of lines. For human exome chip, you are like to see 10k lines in this file. That means out of total 250k variants, around 10k SNP variants have allele frequency larger than 0.5.

.check.mono file

This file contains the monomorphic sites. It is normal that this files contains a number of lines. In the ideal case, VCF files should only contain variant sites. However, it is practical or convenient to keep some monomorhipc sites in the VCF file. This file records the number of monomorphic sites.


Questions or comments can be sent to Xiaowei Zhan or Dajiang Liu.