https://github.com/mehelmy/hifitargetenrichmentqc

QC scripts for the Twist Alliance Dark Genes Panel
https://github.com/mehelmy/hifitargetenrichmentqc

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QC scripts for the Twist Alliance Dark Genes Panel

• Host: GitHub
• URL: https://github.com/mehelmy/hifitargetenrichmentqc
• Owner: MeHelmy
• License: bsd-3-clause
• Created: 2024-03-12T15:59:38.000Z (10 months ago)
• Default Branch: main
• Last Pushed: 2024-03-12T16:35:55.000Z (10 months ago)
• Last Synced: 2024-03-12T17:30:56.325Z (10 months ago)
• Language: Python
• Size: 28.3 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# HiFiTargetEnrichmentQC

QC scripts for the Twist Alliance Dark Genes Panel

This is a Snakemake script to benchmark data output per gene. The data required to run the benchmark are:

1. Bam file

2. Phased SNVs and Indels file

3. SVs file

For Snakemake to run, naming conventions need to be followed:

1. Create a link to the bam file.

2. Create a link to the SV VCF file, e.g., HG002.SVs.vcf. NOTE: The first part of the name must match the bam file name, so in this case, HG002.

3. Create a SNVs directory, e.g., mkdir -p HG002_SNVs. NOTE: The first part of the name must match the bam file name, so in this case, HG002.

4. In the previous directory, link the SNVs file with the following name: phased_merge_output_AF_filtered.vcf.gz. Also link the phased_merge_output_AF_filtered.vcf.gz.tbi.

An example of how to run the script:

The `HG002.stat` is an example of the output needed. Replace HG002 with your sample name if needed.