ncov-parser 0.7.0

A nCoV package for parsing analysis files

ncov_parser

The ncov_parser package provides a suite of tools to parse the files generated in the Nextflow workflow and provide a QC summary file. The package requires several files including:

• .variants.tsv
• .variants.norm.vcf
• .pass.vcf
• .per_base_coverage.bed
• .primertrimmed.consensus.fa
• .consensus.fasta
• alleles.tsv

An optional metadata file with qPCR ct and collection date values can be included.

In addition, bedtools should be run to generate a <sample>.per_base_coverage.bed file to generate mean and median depth of coverage statistics.

Installation

After downloading the repository, the package can be installed using pip:

git clone https://github.com/jts/ncov-tools
cd ncov-tools/parser
pip install .

Usage

The library consists of several functions that can be imported.

import ncov.parser

Several classes are available representing the different files that can be processed.

ncov.parser.Alleles
ncov.parser.Consensus
ncov.parser.Lineage
ncov.parser.Meta
ncov.parser.PerBaseCoverage
ncov.parser.Snpeff
ncov.parser.Variants
ncov.parser.Vcf
ncov.parser.primers

Similarly, wrapper scripts for creating a standard format output can be found in ncov.parser.qc

import ncov.parser.qc as qc
qc.write_qc_summary_header()
qc.write_qc_summary()

Top levels scripts

In the bin directory, several wrapper scripts exist to assist in generating QC metrics.

To create sample level summary qc files, use the get_qc.py script:

get_qc.py --variants <sample>.variants.tsv or <sample>.pass.vcf
--coverage <sample>.per_base_coverage.bed --meta <metadata>.tsv
--consensus <sample>.primertrimmed.consensus.fa [--indel] --sample <samplename>
--platform <illumina or oxford-nanopore> --run_name <run_name> --alleles alleles.tsv
--indel --lineage <Pangolin lineage report> --aa_table <SNPEff annotation table>

Note the --indel flag should only be present if indels will be used in the calculation of variants.

Once this is complete, we can use the collect_qc_summary.py script to aggregate the sample level summary files into a single run tab-separate file.

collect_qc_summary.py --path <path to sample.summary.qc.tsv files>

To create an amplicon BED file from a primer scheme BED file:

primers_to_amplicons.py --primers <path to primer scheme BED file>
--offset <number of bases to offset> --bed_type <full or no_primers or unique_amplicons>
--output <full path to file to write BED data to>

Credit and Acknowledgements

Note that this tool has been used in conjunction with the @jts ncov-tools suite of tools.

BED file importing and amplicon site merging obtained from the ARTIC pipeline: https://github.com/artic-network/fieldbioinformatics/blob/master/artic/vcftagprimersites.py

License

MIT