From ca2236a0d5b15f19c530afca030b596800735ef9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= Date: Thu, 5 Dec 2024 14:21:55 +0000 Subject: [PATCH] add bcf to input --- README.md | 4 ++-- assets/schema_input.json | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 9478981..39daff6 100644 --- a/README.md +++ b/README.md @@ -50,9 +50,9 @@ Applying filtering on the process of benchmarking itself might makes it impossib 10. Include or exclude SNVs and INDELs ([bcftools filter](https://samtools.github.io/bcftools/bcftools.html#filter)) 11. Size and quality filtering for SVs ([SURVIVOR filter](https://github.com/fritzsedlazeck/SURVIVOR/wiki)) -### Liftover of truth sets: +### Liftover of vcfs: -This sub-workflow provides option to convert genome coordinates of truth VCF and high confidence BED file to a new assembly. Golden standard truth files are build upon specific reference genomes which makes the necessity of lifting over depending on the test VCF in query. +This sub-workflow provides option to convert genome coordinates of truth VCF and high confidence BED file to a new assembly. Golden standard truth files are build upon specific reference genomes which makes the necessity of lifting over depending on the test VCF in query. Lifting over one or more test vcfs is also possible. 12. Create sequence dictionary for the reference ([picard CreateSequenceDictionary](https://gatk.broadinstitute.org/hc/en-us/articles/360037068312-CreateSequenceDictionary-Picard)). This file can be saved and reused. 13. Lifting over truth variants ([picard LiftoverVcf](https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard)) diff --git a/assets/schema_input.json b/assets/schema_input.json index c6a6cf1..0839b98 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -10,9 +10,9 @@ "test_vcf": { "type": "string", "exists": true, - "pattern": "\\S+\\.vcf(\\.gz)?$", + "pattern": "\\S+\\.(vcf|bcf)(\\.gz)?$", "format": "file-path", - "errorMessage": "Test VCF must be provided, cannot contain spaces and must have extension '.vcf.gz' or '.vcf'", + "errorMessage": "Test VCF must be provided, cannot contain spaces and must have extension '.vcf.gz', '.vcf', '.bcf.gz' or 'bcf'", "description": "The VCF file to use as benchmarking test input" }, "id": {