Collection of random utility scripts for processing ARTIC sequencing results

This script will process each alignment in a BAM file and output which base each read supports at a particular reference position. Reads that do not cover the reference position are reported as N. I use this script to debug primer trimming and amplification artifacts. The coordinates output (fragment_start, fragment_end) are for the entire paired-end fragment, not the individual reads. This is to help visualize reads that cross amplicon boundaries.

Example usage:

python extract_evidence_reads.py --bam input.bam --position 17747

Output:

sample_name     read_name       fragment_start  fragment_end    fragment_length base
sample_abcd     read_1          17744           18103           359             T

This script compares collections of ivar .variants.tsv files to detect variants that are unique to one collection, or significantly changed variant allele frequency. I use this to evaluate the effects of changing pipeline versions.

Example usage:

find pipeline_v1.5_results -name "*.variants.tsv" > v1.5.fofn
find pipeline_v1.6_results -name "*.variants.tsv" > v1.6.fofn
python compare_variant_calls.py -a-fofn v1.5.fofn -b-fofn v1.6.fofn -a-name v1.5 -b-name v1.6

It is recommended that you filter the results list of variant calling differences to remove samples that fail QC (e.g. <90% completeness).

This script will recursively search a directory structure for variants files (ivar variant.tsv files, or nanopore .pass.vcf.gz files) and print out any samples that match a variant in watchlist.vcf. Example:

python ncov-watch.py --watchlist /path/to/watchlist.vcf --directory data 2>/dev/null

Alternatively you can pass the variant files on stdin:

find data/ -name "*.variants.tsv" | python ncov-watch.py --watchlist /path/to/watchlist.vcf 2>/dev/stderr

(note 2>/dev/stderr is to silence pysam warnings when parsing VCF files)