benchmarking-tools

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I am getting a CalledProcessError regarding the benchmark vcf, even though it has been indexed. ``` 2021-05-05 18:27:33,391 WARNING No reference file found at default locations. You can set the...

gmykim

Benchmarking my dataset

2

Hi, I want to benchmark my variant calls (not GIAB or platinum dataset). How should i do with the help of this tool? Thanks

raman91

Bumps [jinja2](https://github.com/pallets/jinja) from 2.8 to 2.11.3. Release notes Sourced from jinja2's releases. 2.11.3 This contains a fix for a speed issue with the urlize filter. urlize is likely to be...

dependabot[bot]

GRCh38 / hg38 stratification BED files

7

Do the BED files under `resources/stratification-bed-files` exist for GRCh38? If so it would be great if they could be added to the repo

blmoore

In the interest of promoting data provenance and reproducibility, I propose to add some headers to the VCF-I spec: ##program= ##comparator= ##truthVCF= ##queryVCF= ##truthRegions= ##targetRegions=

jdidion

Truth set high-confidence regions and shiftable indels

2

Gold standard benchmarking datasets such as the GIAB/NIST NA12878 and the Illumina Platinum Genomes truth sets provide both a VCF containing the variant records themselves, plus a BED file of...

Lenbok

Standardizing performance metrics output file

4

Since we're getting close to outputting performance metrics, I thought we should have a discussion around the output format, which will allow us to exchange outputs from different comparison workflows...

jzook

Records in intermediate VCF format

3

Apologies for jumping into this discussion late. My question is what are the records in the intermediate VCF format? e.g. given two inputs _Truth_ > 1 10 AT GT,AC 0/1...

bioinformed