Benchmarking my dataset

[raman91]

Hi,

I want to benchmark my variant calls (not GIAB or platinum dataset). How should i do with the help of this tool?

Thanks

[pkrusche]

Hi,

I think hap.py should work with other datasets also -- you need these files minimally:

• a truth VCF file
• a query VCF file
• a reference FASTA file that matches the two files above

An example command line for running hap.py on these files is given here:

https://github.com/illumina/hap.py#haplotype-comparison-tools

Optionally you can also give a set of confident hom-ref regions using the -f switch -- when these are not specified, every call in the query that is not matched by the truth will count as a false positive.

Hope this is helpful!

[aditya-sarkar441]

@pkrusche hap.py belongs to the Illumina. How can I run your tool on my input file ? There is no mention in the documentation on how we can compile your tool on our files.