I'm wondering if there's a simple way to convert directly from mpileup format to vcf without having to go through all the steps of creating a bam files to bcf to vcf etc. https://www.ebi.ac.uk/sites/ebi.ac.uk/files/content.ebi.ac.uk/materials/2014/140217_AgriOmics/dan_bolser_snp_calling.pdf
I just want the variable sites from the mpileup file in vcf format.
I tried this and didn't work (Generating Both Pileup And Vcf/Bcf Using Samtools Mpileup)
bcftools view -v -c file.mpileup > file.vcf