hap.py
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Illumina
Haplotype VCF comparison tools
In other words, if you have a query VCF in the form `my.vcf.gz`, and you set `-o my`, your `my.vcf.gz` will be silently over-written on completion. It seems also that...
Running hap.py with HG38 vcfs and an HG38 reference and outputting an annotated vcf, the evaluation appears to use the correct reference, however the dictionary in the output vcf header...
I experienced this error: [W] Found a variant with more 4 > 2 (max) alt alleles. These become no-calls.
At https://github.com/Illumina/hap.py/blob/6c907ce3b02956bc239022db6edea7c48d6ddb8b/src/c++/lib/variant/VariantReader.cpp#L735, the size allocated for the array `ad` is `adcount`, whereas in the function https://github.com/Illumina/hap.py/blob/6c907ce3b02956bc239022db6edea7c48d6ddb8b/src/c++/lib/tools/BCFHelpers.cpp#L532 (which gets called at VarientReader:738 with `ad`) writes `values.size()` elements ( where `values` is...
Hi, Is it possible to use hap.py to make allele only comparisons? (i.e. Can the genotype check be disabled?). I know som.py does this, but I'd like to keep hap.py's...
Hi hap.py authors: I think I may have run into a bug in happy, but I'm not 100% certain. Here's the example: query: 20 57777379 . C CT 0 ....
I have a file (attached, [repro.vcf.gz](https://github.com/Illumina/hap.py/files/1659505/repro.vcf.gz)) which will consistently cause a segmentation fault in `preprocess` when running `pre.py`. The problem can be reproduced with the latest `pkrusche/hap.py` Docker image by...
Hi Happy authors, We've been using hap.py for our internal DeepVariant evaluations and recently did a deep dive into some of the FPs and FNs and discovered what looks like...
In our deep dive into happy with DeepVariant we've noticed that hap.py includes in its confident calls for comparison any multi-base event (e.g., a deletion) that merely overlaps with the...
The default ubuntu-based docker image is built using the default Python libraries from Ubuntu's repo, which for the pysam library are very outdated. This breaks the Tools/bamstats.py module, which calls...
