Peter Krusche
Peter Krusche
TS_boundary would capture all variants that overlap with but aren't fully contained within the confident regions. TS_contained has all variants that are fully contained within the confident regions. For insertions,...
Can you compile any c++ code on your system? Seems like libstdc++ isn't installed?
Hi Rohan, the QQ field should (most of the time) be a direct translation of the DP field in the original (query) VCF file. I think there is some logic...
Thanks! I'll change the pysam method of installation to pip for the next release.
Which Python version are you using? hap.py / som.py won't work with Python 3.
I think we discussed this in the GA4GH benchmarking group and the conclusion was that this is more of a truthset rather than a comparison issue. Hap.py does stratify these...
This is probably the result of hap.py 'fixing' the confident regions after preprocessing the truth VCF (the corresponding command line options are `--adjust-conf-regions` and `--no-adjust-conf-regions`, the default is on to...
At this point, pre.py cannot do this. Depending on the interpretation of 0/0 this can be quite a tricky problem: if we assume 0/0 to mean "reference with no SNP...
Thanks for the report! I think the temporary workaround for this would be to use bcftools annotate to remove AD (which isn't used by hap.py). In the future, the code...
Hi Katie, 1) the environment variable HGREF is set outside the Docker image to a location not accessible from within. The location needs to be relative to a path mounted...