diff --git a/docs/Updates.md b/docs/Updates.md index 3f3667d..c2af743 100644 --- a/docs/Updates.md +++ b/docs/Updates.md @@ -1,6 +1,19 @@ -# Truvari 5.1.1 +# Truvari 5.2.1 *in progress* +* Fixed FP BNDs being dropped [details](https://github.com/ACEnglish/truvari/discussions/263). + +# Truvari 5.2.0 +*February 16, 2025* + +* The default `--align` method for `phab` and `bench` switched to POA. See [discussion](https://github.com/ACEnglish/truvari/discussions/261) for details. +* Fix bug in `--pick ac` where FN/FP variants were not being counted/output. +* Fix `--dup-to-ins` Ticket [#258](https://github.com/ACEnglish/truvari/issues/258) +* `ga4gh` now also writes a variant count summary json + +# Truvari 5.1.1 +*February 5, 2025* + * `bench` * new automatic hook into the refine step via `truvari bench --refine` * `refine` diff --git a/docs/bench.md b/docs/bench.md index 5352c60..ebbcb5e 100644 --- a/docs/bench.md +++ b/docs/bench.md @@ -149,13 +149,18 @@ Refining bench output ===================== As described in the [[refine wiki|refine]], a limitation of Truvari bench is 1-to-1 variant comparison. However, `truvari refine` can harmonize the variants to give them more consistent representations. A bed file named `candidate.refine.bed` is created by `truvari bench` and holds a set of regions which may benefit from refinement. To use it, simply run ```bash -truvari bench -b base.vcf.gz -c comp.vcf.gz -o result/ -truvari refine --regions result/candidate.refine.bed \ - --reference reference.fasta \ - --recount --use-region-coords \ - result/ +truvari bench -b base.vcf.gz -c comp.vcf.gz --reference reference.fasta -o result/ +truvari refine result/ +``` + +Refine has a few parameters detailed in the [[refine wiki|refine]]. But if you'd ike to run refinement automatically with defaults, you can simply use +```bash +truvari bench -b base.vcf.gz + -c comp.vcf.gz + --reference reference.fasta + -o result/ + --refine ``` -See [[refine wiki|refine]] for details. Comparing Sequences of Variants =============================== diff --git a/truvari/collapse.py b/truvari/collapse.py index 98259fb..65d51ff 100644 --- a/truvari/collapse.py +++ b/truvari/collapse.py @@ -482,7 +482,7 @@ def parse_args(args): filteg.add_argument("-s", "--sizemin", type=truvari.restricted_int, default=50, help="Minimum variant size to consider for comparison (%(default)s)") filteg.add_argument("-S", "--sizemax", type=truvari.restricted_int, default=50000, - help="Maximum variant size to consider for comparison (%(default)s)") + help="Maximum variant size to consider for comparison (-1 = off; %(default)s)") filteg.add_argument("--passonly", action="store_true", default=False, help="Only consider calls with FILTER == PASS") diff --git a/truvari/variant_params.py b/truvari/variant_params.py index 6684f6d..4407a66 100644 --- a/truvari/variant_params.py +++ b/truvari/variant_params.py @@ -85,7 +85,7 @@ class VariantParams(): "bnddist": 100, "sizemin": 50, "sizefilt": 30, - "sizemax": -1, + "sizemax": 50000, "passonly": False, "no_ref": False, "pick": "single",