This pipeline converts seekdeep output files generated by Nick Hathaway's seekdeep program into VCF files and amino acid tables suitable for easy graphing, e.g. with github.com/simkin-bioinformatics/AA_table_visualization. The pipeline assumes that you have snakemake, singularity, and Nick's elucidator.sif file already installed on your system. Example inputs are provided in the yaml file.
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bailey-lab/haplotype_variant_calling
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uses Nick Hathaway's variantCallOnSeqAndProtein script to call variants on vcf files and generate prevalences and amino acid calls
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