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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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