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.
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 .
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()
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>
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
MIT