zhanxw/checkvcf

Sanity check Variant Call Format (VCF) files.

checkvcf's Issues

VCF does not have correct column number

Hi, I am using checkVCF and got the error Line [ 1 ] does not have correct column number, exiting!. I checked the columns by reading first several lines into python and split them by \t, which gave me the same column number. I did not encounter this when processing other datasets.
How can I fix this?
Many thanks

Mismatch REFBase

Dear all,

I tried to use CheckVCF.py with the hg38 fasta (from UCSC) and the report gave me an enormous amount of MismatchRefBase Inconsistent reference sites. When looking for check.ref file noticed that all those variants are in lower case in the fasta file and that's the reason why it gives that warning.

Upgrade to python3?

Are you planning any updates to python 3?

Here's an attempt - but it's best you verify the contents...
checkVCF.python39.py.zip

Expects format column in all VCFs

According to VCF specification the "FORMAT" column is not mandatory:
http://samtools.github.io/hts-specs/VCFv4.2.pdf
This script fails due to line 219, that always expects a format column.

logs

Hi,

When running this in a for-loop for each chromosome, the out.* file will constantly be overridden, will it not? In either case, it would be great if there is a flag to name those out.* files, or if the out.* file is automatically named after the base name of the input files. For example: cohort1.chr1.vcf.gz would lead to cohort1.chr1.out.*

Thanks!

Sander

Error asking to clean VCF, which I already did

I get the following error,
Please use the following command to clean your VCF file and then re-run checkVCF.py
(grep ^"#" $your_old_vcf; grep -v ^"#" $your_old_vcf | sed 's:^chr::ig' | sort -k1,1n -k2,2n) | bgzip -c > $your_vcf_file

Not sure how to fix this. This code does not do anything.
I am trying to check against hg38 version. Therefore, chromosomes were coded as in hg38.fa file. I see that the same VCF file works when chromosomes were coded continuously but does not serve the purpose. Please suggest how I can solve this problem. I aim to perform imputation.

Splitting columns by whitespace

VCF file is tab-delimited according to the specification.

The following line is splitting the header line by whitespace:

https://github.com/zhanxw/checkVCF/blob/master/checkVCF.py#L194

If sample name contains space, incorrect number of columns will be counted.