Comments (2)
cc2qe
commented on July 28, 2024
I don't have much experience with different versions of ROOT, but we're using v5.34.20 on our system so I can confirm it works with that. I don't have any ideas for the TFrame error other than those mentioned in the seqanswers thread, but I would attempt to install the standard version of CNVnator first to simplify troubleshooting. If your ROOT install cooperates with the standard CNVnator then it should also work with SpeedSeq's version.
SpeedSeq primarily uses CNVnator to annotate the read-depth of variants that were discovered by LUMPY. This adds a "CN" field to the genotypes of each sample in the VCF. It also produces a separate BED file with the suffix ".sv.readdepth.bed" with the copy number intervals produced by CNVnator.
from speedseq.
ragans
commented on July 28, 2024
colby,
Thanks very much for the details. I'll continue to work with our admins to try to get the build right.
It's fine to close this issue.
Thanks again for your help and the quick response.
Kind regards,
Seamus Ragan
from speedseq.
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