Input file has no samples. Hap.py will not like that. about hap.py

[pkrusche]

You could set a genotype using bcftools annotate or run hap.py with --set-gt hom. Hap.py also includes a tool called alleles in the truth folder which can add genotype fields.

Note that hap.py will compare genotypes, so when setting truth genotypes to a particular value it will be a good idea to also do this for the query ones (--set-gt does that). This affects how the comparison is done:

• --set-gt hom will require all alleles to be on the same haplotype. Overlapping alleles will lead to mismatches
• --set-gt het allows for alleles to overlap by assigning them to maximally two haplotypes (i.e. three overlapping alleles will cause FPs).
• vcfeval has an option called squash-ploidy. This option is similar to --set-gt hom but will only require one allele per VCF record to match for a TP (i.e. multiple alleles are treated as alternate hypotheses). Hap.py doesn't support passing this option to vcfeval currently, but this could be added quite easily.

Some discussion on this is here also: #42

[afzm]

Thank you I formatted the golden.vcf to the format of a vcf file from a variant caller and it worked.

[pkrusche]

Great, happy to help!