checkVCF
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zhanxw
Sanity check Variant Call Format (VCF) files.
Are you planning any updates to python 3? Here's an attempt - but it's best you verify the contents... [checkVCF.python39.py.zip](https://github.com/zhanxw/checkVCF/files/14694998/checkVCF.python39.py.zip)
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' |...
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...
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...
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...
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.
Dear all, I tried to use CheckVCF.py with the hg38 fasta (from [UCSC](http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/)) and the report gave me an enormous amount of MismatchRefBase Inconsistent reference sites. When looking for check.ref...
