iarcbioinfo/vcf-isec-nf
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iarcbioinfo/vcf-isec-nf repository overview
Nextflow VCF Intersection Pipeline
Description
This Nextflow pipeline performs the intersection of VCF files using bcftools used in Mangiante et al. 2023. It takes genomic VCF files (for example from Mutect and Strelka), extracts SNVs from the first caller, intersects results from the two callers for indels and multinucleotide polymorphisms (MNPs), and creates a concatenated, indexed VCF file containing SNPs from variant caller 1 and intersected indels/MNPs.
Dependencies
- This pipeline is based on Nextflow. Please refer to the IARC-nf repository for installation, basic usage, and configuration information for Nextflow and our pipelines.
- External software:
- bcftools
You can avoid installing all the external software by only installing Docker. See the IARC-nf repository for more information.
Input
| Type | Description |
|---|---|
| input_folder1 | Path to the folder containing VCF files (e.g., outputs from IARCbioinf/mutect2-nf) |
| input_folder2 | Path to the folder containing other VCF files (e.g., from IARCbioinf/strelka2-nf) |
Parameters
-
Optional
| Name | Default value | Description |
|---|---|---|
| --output_folder | output/ | Path of the output folder |
| --vcfSuffix1_snvs | _filtered_PASS_norm.vcf.hg38_multianno.vcf.gz | Suffix of first SNV VCF files |
| --vcfSuffix1_indels | _filtered_PASS_norm.vcf.hg38_multianno.vcf.gz | Suffix of first indel VCF files |
| --vcfSuffix2_snvs | .somatic.snvs_norm.vcf | Suffix of second SNV VCF files |
| --vcfSuffix2_indels | .somatic.indels_norm.vcf | Suffix of second indel VCF files |
Of note, if SNV and indel suffixes for the first or second set of VCFs are different, they are first merged; for example, by default strelka snv and indel VCFs are merged but mutect VCFs are assumed to contain all types of variants.
-
Flags
Flags are special parameters without a value.
| Name | Description |
|---|---|
| --help | Display help |
Usage
nextflow run IARCbioinfo/VCF-isec-nf --input_folder1 Mutect_results/ --input_folder2 strelka_results/ --outputFolder Mutect_strelka_intersection
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over 3 years ago
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