Len Trigg

Try using the vcfeval engine. It will find the match as long as --ref-overlap is used (which I believe that hap.py does). ```` ##fileformat=VCFv4.1 ##fileDate=20180203 ##source=RTG Tools 3.8.4 / Core...

I made a quick test case for these input variants and vcfeval will output the following ga4gh intermediate formatted match (give or take other annotations): ```` 20 16392574 . C...

That usually means the vcf in question is not self-consistent, e.g. not all of the asserted variants can be simultaneously possible in a diploid genome. In a few cases it...

You can always try running RTG vcfeval directly if you don't need stratification.

How do you normalize a 0/0 or ./. variant?

In general this is not possible, because the act of normalizing variants of non-REF genotypes can mean that it is no longer valid to retain other sites that were reported...

See the format definitions: https://github.com/ga4gh/benchmarking-tools/blob/master/doc/ref-impl/intermediate.md https://github.com/ga4gh/benchmarking-tools/blob/master/doc/ref-impl/outputs.md `BD=N` means the variant was not assessed, for example it is outside the evaluation regions, or excluded for other reasons. In the case of...

Have you tried using vcfeval instead of xcmp as the comparison engine?

Usually that vcfeval message means your VCFs are using chromosome names like "1", "2", etc but the reference SDF has names like "chr1", "chr2", etc (or vice versa). Note that...

@DBS-Max The error message looks to be complaining about filter value "q10,LBQ". Multiple filter values should be separated by semicolon, not comma. Check whether this malformed filter value is in...