Output table of snps for each sample

ellisrichardj / BovTB-nf

Nextflow script for processing WGS data

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Closed ellisrichardj closed 4 years ago

ellisrichardj commented 4 years ago

A snp table similar to those produced by snippy would be a useful additional output.

ellisrichardj commented 4 years ago

Ideally use existing tools to generate (bcftools?)

ellisrichardj commented 4 years ago

Need to fix compatibility issues with current vcf format

ellisrichardj commented 4 years ago

Need bcftools to write RO and AO values (number of reads with reference or alternate base) into VCF