Comments (3)
Are you using default parameters? If so, there are size parameters which may be removing SVs.
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Yes, I am using default parameters. Are you referring to the "pctsize" parameter?
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No, I'm referring to the size parameters https://github.com/ACEnglish/truvari/wiki/bench#difference-between---sizemin-and---sizefilt as described in the documentation
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Related Issues (20)
- error from collapse function : TypeError: invalid value for Integer format HOT 2
- Can't install via conda or pip HOT 2
- Error with Truvari collapse from bcftools-merged Manta VCFs HOT 1
- --choose behavior HOT 5
- Output from truvari bench command HOT 13
- Error building Docker image HOT 1
- SVLEN conversion error HOT 3
- some tests failed on macOS HOT 3
- GT-precision calculation HOT 3
- 'Structural' is spelled wrong in the first line of the README
- TypeError: values expected to be 2-tuple, given len=1 HOT 2
- Same Variant appears in both TP sets and in FN or FP set. HOT 4
- Are "TP-base" and "TP-comp" always the same value? HOT 1
- Error while installing on macOS M2 (Silica chipset) HOT 3
- The SVLEN and -m flag have somewhat unexpected behavior when REF and ALT are both long HOT 2
- Handling of symbolic variants without ref sequence HOT 1
- Truvari phab fails to read VCF headers from output file and crashes HOT 4
- Truvari refine hangs indefinitely HOT 5
- TP considered FN HOT 5
- Unable to install because of bwapy wheel build failure on MacOS HOT 1
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