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‎README.md‎

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# TronFlow VCF postprocessing
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![GitHub tag (latest SemVer)](https://img.shields.io/github/v/release/tron-bioinformatics/tronflow-variant-normalization?sort=semver)
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[![Run tests](https://github.com/TRON-Bioinformatics/tronflow-variant-normalization/actions/workflows/automated_tests.yml/badge.svg?branch=master)](https://github.com/TRON-Bioinformatics/tronflow-variant-normalization/actions/workflows/automated_tests.yml)
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![GitHub tag (latest SemVer)](https://img.shields.io/github/v/release/tron-bioinformatics/tronflow-vcf-postprocessing?sort=semver)
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[![Run tests](https://github.com/TRON-Bioinformatics/tronflow-vcf-postprocessing/actions/workflows/automated_tests.yml/badge.svg?branch=master)](https://github.com/TRON-Bioinformatics/tronflow-vcf-postprocessing/actions/workflows/automated_tests.yml)
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[![DOI](https://zenodo.org/badge/372133189.svg)](https://zenodo.org/badge/latestdoi/372133189)
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[![License](https://img.shields.io/badge/license-MIT-green)](https://opensource.org/licenses/MIT)
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[![Powered by Nextflow](https://img.shields.io/badge/powered%20by-Nextflow-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://www.nextflow.io/)
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* Technical annotations from different BAM files
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* Functional annotations
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## How to run it
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Run it from GitHub as follows:
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```
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nextflow run tron-bioinformatics/tronflow-vcf-postprocessing -r v2.1.0 -profile conda --input_vcfs input_vcfs --reference reference.fasta
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```
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Otherwise download the project and run as follows:
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```
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nextflow main.nf -profile conda --input_vcfs input_vcfs --reference reference.fasta
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```
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Find the help as follows:
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```
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$ nextflow run tron-bioinformatics/tronflow-vcf-postprocessing --help
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TronFlow VCF normalization v${VERSION}
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Usage:
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nextflow run main.nf --input_vcfs input_vcfs --reference reference.fasta
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Input:
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* --input_vcf: the path to a single VCF to normalize (not compatible with --input_files)
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* --input_vcfs: the path to a tab-separated values file containing in each row the sample name and path to the VCF file (not compatible with --input_vcf)
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The input file does not have header!
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Example input file:
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sample1 /path/to/your/file.vcf
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sample2 /path/to/your/file2.vcf
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* --reference: path to the FASTA genome reference (indexes expected *.fai, *.dict)
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* --vcf-without-ad: indicate when the VCFs to normalize do not have the FORMAT/AD annotation
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Optional input:
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* --output: the folder where to publish output
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* --skip_decompose_complex: flag indicating not to split complex variants (ie: MNVs and combinations of SNVs and indels)
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* --filter: specify the filter to apply if any (e.g.: PASS), only variants with this value will be kept
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* --input_bams: a tab-separated values file containing in each row the sample name, tumor and normal BAM files for annotation with Vafator
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* --snpeff_organism: the SnpEff organism name (eg: hg19, hg38, GRCh37.75, GRCh38.99)
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* --snpeff_datadir: the SnpEff data folder where the reference genomes were previously downloaded. Required if --snpeff_organism is provided
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* --snpeff_args: additional SnpEff arguments
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Output:
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* Normalized VCF file
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* Tab-separated values file with the absolute paths to the normalized VCF files, normalized_vcfs.txt
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* Summary statistics before and after normalization
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```
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### Input tables
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The table with VCF files expects two tab-separated columns without a header
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| Patient name | VCF |
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|----------------------|------------------------------------------------------------------------|
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| patient_1 | /path/to/patient_1.vcf |
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| patient_2 | /path/to/patient_2.vcf |
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The optional table with BAM files expects two tab-separated columns without a header.
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| Patient name | Sample name:BAM |
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|----------------------|---------------------------------|
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| patient_1 | primary_tumor:/path/to/sample_1.primary.bam |
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| patient_1 | metastasis_tumor:/path/to/sample_1.metastasis.bam |
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| patient_1 | normal:/path/to/sample_1.normal.bam |
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| patient_2 | primary_tumor:/path/to/sample_1.primary_1.bam |
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| patient_2 | primary_tumor:/path/to/sample_1.primary_2.bam |
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| patient_2 | metastasis_tumor:/path/to/sample_1.metastasis.bam |
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| patient_2 | normal:/path/to/sample_1.normal.bam |
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Each patient can have any number of samples. Any sample can have any number of BAM files, annotations from the
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different BAM files of the same sample will be provided with suffixes _1, _2, etc.
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The aggregated vafator annotations on each sample will also be provided without a suffix.
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## Variant filtering
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Optionally, only variants with the value in the column `FILTER` matching the value of parameter `--filter` are kept.
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otherwise defaults will be used.
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## How to run it
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Run it from GitHub as follows:
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```
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nextflow run tron-bioinformatics/tronflow-variant-normalization -r v2.0.0 -profile conda --input_vcfs input_vcfs --reference reference.fasta
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```
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Otherwise download the project and run as follows:
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```
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nextflow main.nf -profile conda --input_vcfs input_vcfs --reference reference.fasta
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```
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Find the help as follows:
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```
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$ nextflow run tron-bioinformatics/tronflow-variant-normalization --help
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TronFlow VCF normalization v${VERSION}
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Usage:
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nextflow run main.nf --input_vcfs input_vcfs --reference reference.fasta
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Input:
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* --input_vcf: the path to a single VCF to normalize (not compatible with --input_files)
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* --input_vcfs: the path to a tab-separated values file containing in each row the sample name and path to the VCF file (not compatible with --input_vcf)
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The input file does not have header!
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Example input file:
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sample1 /path/to/your/file.vcf
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sample2 /path/to/your/file2.vcf
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* --reference: path to the FASTA genome reference (indexes expected *.fai, *.dict)
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* --vcf-without-ad: indicate when the VCFs to normalize do not have the FORMAT/AD annotation
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Optional input:
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* --output: the folder where to publish output
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* --skip_decompose_complex: flag indicating not to split complex variants (ie: MNVs and combinations of SNVs and indels)
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* --filter: specify the filter to apply if any (e.g.: PASS), only variants with this value will be kept
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* --input_bams: a tab-separated values file containing in each row the sample name, tumor and normal BAM files for annotation with Vafator
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Output:
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* Normalized VCF file
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* Tab-separated values file with the absolute paths to the normalized VCF files, normalized_vcfs.txt
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* Summary statistics before and after normalization
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```
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### Input tables
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The table with VCF files expects two tab-separated columns without a header
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| Patient name | VCF |
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|----------------------|------------------------------------------------------------------------|
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| patient_1 | /path/to/patient_1.vcf |
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| patient_2 | /path/to/patient_2.vcf |
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The optional table with BAM files expects two tab-separated columns without a header.
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| Patient name | Sample name:BAM |
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|----------------------|---------------------------------|
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| patient_1 | primary_tumor:/path/to/sample_1.primary.bam |
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| patient_1 | metastasis_tumor:/path/to/sample_1.metastasis.bam |
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| patient_1 | normal:/path/to/sample_1.normal.bam |
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| patient_2 | primary_tumor:/path/to/sample_1.primary_1.bam |
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| patient_2 | primary_tumor:/path/to/sample_1.primary_2.bam |
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| patient_2 | metastasis_tumor:/path/to/sample_1.metastasis.bam |
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| patient_2 | normal:/path/to/sample_1.normal.bam |
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Each patient can have any number of samples. Any sample can have any number of BAM files, annotations from the
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different BAM files of the same sample will be provided with suffixes _1, _2, etc.
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The aggregated vafator annotations on each sample will also be provided without a suffix.
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## References
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* Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. Unified Representation of Genetic Variants. Bioinformatics (2015) 31(13): 2202-2204](http://bioinformatics.oxfordjournals.org/content/31/13/2202) and uses bcftools [Li, H. (2011). A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics (Oxford, England), 27(21), 2987–2993. 10.1093/bioinformatics/btr509

‎nextflow.config‎

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* --filter: specify a comma-separated list of filters to apply (e.g.: PASS,.), only variants with these values will be kept. If not provided all varianst are kept
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* --vcf-without-ad: indicate when the VCFs to normalize do not have the FORMAT/AD annotation
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* --input_bams: a tab-separated values file containing in each row the sample name, tumor and normal BAM files for annotation with Vafator
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* --snpeff_organism: the SnpEff organism name (eg: hg19, hg38, GRCh37.75, GRCh38.99)
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* --snpeff_datadir: the SnpEff data folder where the reference genomes were previously downloaded. Required if --snpeff_organism is provided
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* --snpeff_args: additional SnpEff arguments
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Output:
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* Normalized VCF file

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