Comments (4)
Could you let me know what parameters you used? They can be found at the head of the bench_result/log.txt
. Something like
2024-02-07 15:45:59,529 [INFO] Params:
{
"base": "benchmark.HG002.GRCh38.norm.vcf.gz",
"comp": "HG002.GRCh38.vcf.gz",
"output": "bench_result",
"includebed": "GIAB-Q100.GRCh38.bed",
"extend": 0,
"debug": false,
"reference": null,
"refdist": 500,
"pctseq": 0.7,
"minhaplen": 50,
"pctsize": 0.7,
"pctovl": 0.0,
"typeignore": true,
"chunksize": 1000,
"bSample": "syndip",
"cSample": "HG002",
"dup_to_ins": true,
"sizemin": 1,
"sizefilt": 1,
"sizemax": 1000,
"passonly": false,
"no_ref": "a",
"pick": "single",
"check_monref": true,
"check_multi": true
}
from truvari.
Here are the parameters:
{
"base": "assembly.svs.vcf.gz",
"comp": "nanovar.vcf.gz",
"output": "truvari_bench/nanovar_hifi",
"includebed": null,
"extend": 0,
"debug": false,
"reference": null,
"refdist": 500,
"pctseq": 0.7,
"minhaplen": 50,
"pctsize": 0.7,
"pctovl": 0.0,
"typeignore": false,
"chunksize": 1000,
"bSample": "HG00171",
"cSample": "HG00171.mm2.sorted",
"dup_to_ins": false,
"sizemin": 50,
"sizefilt": 30,
"sizemax": 50000,
"passonly": true,
"no_ref": false,
"pick": "single",
"check_monref": true,
"check_multi": true
}
from truvari.
Hi,
So the "pctseq": 0.7,
is the problem here. Truvari needs sequence resolved variants to calculate sequence similarity. If sequence similarity is on, then symbolic alts are filtered out (there should be a warning in the log file). If you turn off sequence similarity with truvari bench --pctseq 0
, then the symbolic alts are not removed.
Have a great day,
~/Adam English
from truvari.
It is fixed when I use --pctseq 0
. Thanks!
from truvari.
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from truvari.