Comments (2)
Your expectations are correct. The VCFs should have as many entries as the counts in the summary.txt. For example, in our testing infrastructure, we see:
$ head summary.txt
{
"TP-base": 7,
"TP-call": 8,
"FP": 9,
"FN": 4,
"precision": 0.47058823529411764,
"recall": 0.6363636363636364,
"f1": 0.5410628019323671,
"base cnt": 11,
"call cnt": 17,
$ grep -vc "#" *.vcf
fn.vcf:4
fp.vcf:9
tp-base.vcf:7
tp-call.vcf:8
If those two commands (head/grep) aren't matching up, I expect there's some sort of problem. Could you double check that those two commands aren't matching up and if not, provide example data so that I can recreate the problem.
from truvari.
Hi! Thanks for your quick reply. That makes sense, I just checked as you suggested using head/grep and I now can't seem to recreate the problem - so I will close the issue for now :) Many thanks for your quick help!
from truvari.
Related Issues (20)
- Question: Does truvari have a upper limit on the file size? How to speed up? HOT 2
- BED Region off-by-one error HOT 4
- Zero matches between base and comp HOT 4
- AttributeError: 'CollapsedCalls' object has no attribute 'consolidate' | version 4.2.1 HOT 4
- Calculate SNV HOT 7
- complex genotype problem HOT 3
- GT integrate HOT 1
- No TP or FP calls for CNV HOT 1
- merging different SV type? HOT 3
- No FP or TP calls HOT 2
- Unable to run MAFFT HOT 9
- md5sum FIPS issue HOT 1
- Support vector for intra-sample merge HOT 6
- some questions about the results in fp.vcf.gz
- 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
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from truvari.