hap.py
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Illumina
Haplotype VCF comparison tools
Are there any plans to support symbolic SVs, or SVs in breakend notation? To properly compare such variants requires haplotype reconstruction as equivalent representations can be quite different. For example,...
I ran hap.py in an interactive shell with singularity here are the commands I used I can't install any modules as I am running this on an HPC environment interactive...
Do you know why the TRUTH.TOTAL differs despite having used the same TRUTH SET?
The error log file as: [E::bgzf_uncompress] inflate failed: invalid distance too far back [E::bgzf_read_block] inflate_block error -1 Number of samples in line and header disagrees at chr2:131765544 2023-12-13 10:11:49,962 ERROR...
Dear @pkrusche and team, I have done an analysis with Deepvariant variants called from a genome in a bottle sample. I did the analysis with hap.py with a singularity pulled...
Hi there I've been following the build from source with CMake; however, at the point in which I launch the following > cmake ../hap.py I'm prompted with the following error...
Use bx-python==0.8.8 to fix ImportError in som.py By default python==0.8.9 is installed and causes the following error: `ImportError: /usr/local/lib/python2.7/dist-packages/bx/intervals/intersection.so: undefined symbol: PyUnicodeUCS2_FromStringAndSize`
Hi, I've been attempting to parse the vcfs generated by the --write-vcf option into R and encountering issues. I believe this has to do with the inconsistency in the number...
Hi there, I am running into an issue while trying to run hap.py using the scmp-distance engine. The relevant output is below: ``` 2023-09-05 06:43:47,418 INFO bcftools index -f -t...
