Comments (2)
Using -f
(--reference
) is the problem here because it needs to fetch reference sequence for every variant. The --reference
parameter has been kept for backwards compatibility, but is no longer recommended. The default 'unroll' sequence comparison technique (details) is faster and also more accurate (see supplementary figure 7).
Try without -f
and --minhaplen
and it should run similarly to --pctseq 0
from truvari.
Also, I see that you're using --keep common
which requires checking variants' genotypes. pysam is pretty slow at accessing genotypes. I just committed a change to develop that reduces how often they need to be accessed. I'm working on a ~50 sample VCF right now and this change is ~2x-5x faster with identical results. So if you'd like to install from develop of the repo, that should help, too. There's also a change to how --gt
is used which helps, but since you're not using that parameter, you won't see the speedup.
from truvari.
Related Issues (20)
- some questions about the results in fp.vcf.gz HOT 1
- Getting same numbers of TP-base and TP-comp HOT 4
- Suggested minor documentation changes
- Truvari, STRs and Expansion Hunter - Query HOT 2
- Bug in benchmarking HOT 4
- Request: truvari collapse --keep option to mantain the ALT sequence HOT 1
- Inquiry on the Determination of Representative Structural Variants in Merged VCF Sets HOT 2
- Truvari Collapse error HOT 1
- Same SV failed to merge HOT 1
- Q: stratify produces all-zero columns HOT 2
- INFO/END field not carried through from input VCF to output VCF HOT 3
- How to handle the "./." genotype in the merged project-level VCF? HOT 2
- Question: meaning of the parameter MINHAPLEN HOT 2
- Collapsed INFO column HOT 1
- wrong collapse? HOT 1
- Issue with MAMnet and Truvari Collapse Parameter Optimization HOT 1
- is it possible to collapse SVs within known groups HOT 7
- Unclear permission denied error when running Truvari bench HOT 5
- "Permission denied: Unknown error" when running truvari in HPC environment HOT 2
- Empty log.txt with Truvari v4.3.1 HOT 2
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from truvari.