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gVCF support, ploidy fixes and usability improvements
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@cyenyxe cyenyxe released this 14 Mar 09:29
v0.7
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Learn about vigilant mode.

The validator can now check fields specific of the gVCF extension. This includes <*> alternate alleles and how they relate to the END INFO field and sample genotypes.

Following some user reports (#101, #102) of incorrect counts being expected for FORMAT fields with Number=G, we confirmed with the specification that their cardinality depends on the ploidy of each sample genotype and not on the ALT column. The issue should be solved now, but if you find any problems please open a new ticket!

This version also introduces some usability improvements. The biggest is a summary report in addition to the existing text and database outputs. This is human-readable and lists each type of error detected, the number of times it occurred, and the first line where it was observed.

The --version option now reports which version of the validator are you running. Please note that in vcf-validator 0.4 or previous this option was used to note which version of the specification the input file should match.

And finally, the validator now warns the user if the input is compressed, instead of reporting a confusing list of errors.

You can download the Linux binaries using the links, and also visit this page if you are interested in the full list of changes.

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