compbio-pysam-variants

Detect nucleotide mutations in pathogen virulence genes by scanning sequencing alignments with pysam. The workflow computes pileup-based variant counts across curated gene sets like mecA for antimicrobial resistance surveillance.

Automate MRSA variant calling by running the call_variants.py script against your BAM alignments and a virulence_genes_ref.json reference. This reports per-gene mutation statistics for resistance-associated genes like mecA.

Yes, pysam pileup variant calling works with curated virulence gene sets defined in a virulence_genes_ref.json reference file. This reference drives the detection and reporting of known mutations across the targeted genes.

Yes, you can use this pathogen variant calling workflow for public health lab genomic screening. It rapidly screens pathogens for resistance-associated variants in curated gene sets, making it suitable for surveillance tasks.

Yes, you need a virulence_genes_ref.json reference file to define genes and known mutations for reporting. This reference is required to perform pileup-based mutation detection across the targeted virulence genes.

A limitation of using pysam for pathogen variant calling is that it focuses strictly on nucleotide differences in genes defined by your reference. Variant detection is pileup-based and requires both Python and pysam to execute the workflow.