lvelosuarez / Sars-CoV-2-NGS-pipeline

A simple snakemake pipeline to call variant from NGS data of Sars-CoV-2 genome

Sars-CoV-2-NGS-pipeline

A simple snakemake pipeline to call variant from NGS data of Sars-CoV-2 genome. It depends on bwa, freebayes, SnpEff/SnpSift and samtools

Installation

You can use conda to install dependencies.

1. git clone https://github.com/dridk/Sars-CoV-2-NGS-pipeline.git
2. conda env create -f environment.yml
3. conda activate covid

You can test the pipeline with our toys dataset :

snakemake -p A.results.csv B.results.csv -j4

Configuration and execution

From config.yml set FASTQ_DIR variable with the folder containing your fastq files. These files must follow the following pattern :

• SAMPLENAME_1.fastq.gz
• SAMPLENAME_2.fastq.gz

To get result of a specific SAMPLENAME:

snakemake -p SAMPLENAME.results.csv

To get fasta genom of a specific SAMPLENAME:

snakemake -p SAMPLENAME.fa

You can pass this consensus sequence to Pangolin to get the lineage.

Results

Each sample comes with a csv file with the following columns :

1. Gene Name
2. Feature ID
3. Variant position
4. Reference bases
5. Alternative bases
6. HGVS coding name
7. HGVS protein name
8. Impact
9. effect

ANN[*].GENE     ANN[*].FEATUREID        POS     REF     ALT     ANN[*].HGVS_C   ANN[*].HGVS_P   ANN[*].IMPACT   ANN[*].EFFECT
ORF1ab  GU280_gp01      490     T       A       c.225T>A        p.Asp75Glu      MODERATE        missense_variant
ORF1ab  YP_009725297.1  490     T       A       c.225T>A        p.Asp75Glu      MODERATE        missense_variant
ORF1ab  YP_009742608.1  490     T       A       c.225T>A        p.Asp75Glu      MODERATE        missense_variant
ORF1ab  GU280_gp01.2    490     T       A       c.225T>A        p.Asp75Glu      MODERATE        missense_variant
ORF1ab  YP_009725298.1  490     T       A       c.-316T>A               MODIFIER        upstream_gene_variant
ORF1ab  YP_009742609.1  490     T       A       c.-316T>A               MODIFIER        upstream_gene_variant
ORF1ab  YP_009725299.1  490     T       A       c.-2230T>A              MODIFIER        upstream_gene_variant
ORF1ab  YP_009742610.1  490     T       A       c.-2230T>A              MODIFIER        upstream_gene_variant