hap.py
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Illumina
Haplotype VCF comparison tools
Encountered similar error mentioned in #178 when running hap.py 0.3.15 installed from Anaconda. After further debugging with ``` preprocess QUERY.vcf.gz:* -l chr9:42008000-42008100 -o QUERY.prep.vcf.gz -V 1 -L 1 -r REF.fa...
I am running hap.py version 0.3.15 and encounter this issue. Some variants are suppose to be FP but they are classified as TP (70k/5mil variants). Have anyone encounter this? ...
I am trying to run `som.py` on two vcfs using `-R`/`-T`option to focus only on certain regions. I got: ```bash 2024-12-02 13:37:32,097 WARNING No reference file found at default locations....
