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inACEnglish/truvari (press backspace or delete to remove)Version : 5.1.1
Describe the bug :
I try to use the truvari anno grm command and have the following error ERROR:root:bwapy isn t available on this machine.
The command is:
truvari anno grm -i data/GCA_947369205.1/GCA_947369205.1_final.vcf ...
ThomasBrazier
- 4
- Opened 10 days ago
- #260
Hi,
Thank you so much for keep updating this wonderful tool!
I am using Truvari to merge SVs for pangenome VCF. In my script, I use truvari API in the following code:
# set up matcher
matcher = truvari.Matcher() ...
Han-Cao
- 2
- Opened 16 days ago
- #259
Version :
Truvari v5.0.0 - built singularity image by converting Dockerfile to singularity definition file. Also occurs when using
a pip install of v5.0.0.
Describe the bug :
SVTYPE=DUP is not being ...
jcslimmer
- 2
- Opened 17 days ago
- #258
Version :
Truvari v5.1.1 384a934b1f9ec53b0668d3046fd03b12cf34b417
Describe the bug :
Truvari bench does not accept --threads argument, refine defaults to 4 threads.
nate-d-olson
- 1
- Opened 19 days ago
- #257
Hi @ACEnglish,
Thank you for creating Truvari—it has been incredibly helpful for SV analysis! However, I encountered an issue with the
recommended bcftools command for truvari collapse outlined on the ...
yueyaog
- 1
- Opened 25 days ago
- #256
Hello,
I ran Truvari to merge tools per sample. The VCF that I got was then implemented in kanpig for genotyping. I encountered
an error
I went back and looked into input files that Truvari used to merge ...
vkaz39
- 11
- Opened on Jan 22
- #255
Thank you for your work. I want to convert gridss to the format needed by Truvari, but I m not sure about the vcf file
lines necessary for Truvari to run. Is it “ALT , SVTYPE=” line? thank you
zhujiahua700403
- 6
- Opened on Jan 13
- #254
Hi Adam,
Happy New Year!
I have (yet another!) question on getting the most intuitive outcomes from truvari with the new GIAB T2T truthset. Based
in part on our previous conversations my current best-practice ...
ctsa
- 6
- Opened on Jan 3
- #252
2024-12-18 11:34:06,792 [INFO] Truvari v4.1.0 2024-12-18 11:34:06,792 [INFO] Command
/home/tigem/h.poddar/miniconda3/envs/truvari/bin/truvari collapse -i
/home/tigem/h.poddar/AF_Calculation/Population_vcf/all_cohort_vcfs_merged.filtered.vcf.gz ...
poddarharsh15
- 9
- Opened on Dec 19, 2024
- #251
Hi Adam,
Thanks again for developing this tool! Great work!
I used truvari bench + refine to benchmark 3 SV callers. Here is what I get from refine.variant_summary.json.
| Tool | Type | Filter | TP-base ...
yangao07
- 3
- Opened on Dec 18, 2024
- #250
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