Add random subsampling as alternative to filtering #39
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SusiJo
reviewed
Jun 18, 2025
SusiJo
reviewed
Jun 18, 2025
SusiJo
reviewed
Jun 18, 2025
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| </details> | ||
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| VCF files can be randomly subsampled to keep only a specific fraction of variants. This enables comparison to the filtered variants. |
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Suggested change
| VCF files can be randomly subsampled to keep only a specific fraction of variants. This enables comparison to the filtered variants. | |
| ### Subsample VCFs | |
| VCF files can be randomly subsampled to keep only a specific fraction of variants. This enables comparison to the filtered variants. |
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I would however suggest to have it like this:
and down below:
Filtering options
String-based filtering
...
Random subset filtering
Co-authored-by: SusiJo <[email protected]>
SusiJo
reviewed
Jun 18, 2025
SusiJo
reviewed
Jun 18, 2025
docs/usage.md
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| > [!NOTE] | ||
| > The filtering step only works with conda for nextflow versions above 24.10.2 (use docker or singularity if you want to use an older nextflow version) | ||
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| ### Subsample VCFs |
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If you change the heading in docs/output.md then please change it here as well.
SusiJo
reviewed
Jun 18, 2025
SusiJo
reviewed
Jun 18, 2025
| process "RANDOMSUBSET" | ||
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| tag "modules" | ||
| tag "modules_" |
SusiJo
approved these changes
Jun 18, 2025
Co-authored-by: SusiJo <[email protected]>
SusiJo
reviewed
Jun 23, 2025
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| ### Subset VCFs | ||
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| VCF files can be randomly subsetted to keep only a specific fraction of variants. This enables comparison to the filtered variants. |
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Suggested change
| VCF files can be randomly subsetted to keep only a specific fraction of variants. This enables comparison to the filtered variants. | |
| VCF files can be randomly selected to keep only a specific fraction of variants. This enables comparison to the filtered variants. |
SusiJo
reviewed
Jun 23, 2025
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| VCF files can be randomly subsetted to keep only a specific fraction of variants. This enables comparison to the filtered variants. | ||
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| You can determine appropriate fractions by comparing the number of filtered variants with the total number of variants. This can be done with a script that collects the number of variants by using `bcftools stats` from both files and dividing them. The more VCF files you use for comparison, the more robust the fraction becomes. (We compared around 90 files and obtained an average fraction of 0.00175 when using `--filter 'INFO/CSQ ~ "HIGH"'`). |
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Suggested change
| You can determine appropriate fractions by comparing the number of filtered variants with the total number of variants. This can be done with a script that collects the number of variants by using `bcftools stats` from both files and dividing them. The more VCF files you use for comparison, the more robust the fraction becomes. (We compared around 90 files and obtained an average fraction of 0.00175 when using `--filter 'INFO/CSQ ~ "HIGH"'`). | |
| You can determine appropriate fractions by comparing the number of filtered variants with the total number of variants. This is done using a script that collects the number of variants with `bcftools stats` from both files and divides the number of variants before and after filtering. The more VCF files are used for comparison, the more robust the fraction becomes. (We compared around 90 files and obtained an average fraction of 0.00175 when using `--filter 'INFO/CSQ ~ "HIGH"'`). |
famosab
commented
Jul 14, 2025
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| - `bcftools/subset/{meta.label}/` | ||
| - `{filename}.subset.vcf.gz`: vcf file with fraction of random variants. | ||
| - `{filename}.seubset.vcf.gz.tbi`: tabix index of the vcf file. |
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Suggested change
| - `{filename}.seubset.vcf.gz.tbi`: tabix index of the vcf file. | |
| - `{filename}.subset.vcf.gz.tbi`: tabix index of the vcf file. |
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I will convert this to draft for now as we decided that the subsampling has to happen at a different stage in the whole analysis workflow. |
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).