This tool enables a user to extract a VCF file out a mpileup file generated from the BAM file using samtools mpileup, for instance. The tool can also stream through STDin so that it is not necessary to store the mpileup file on disk. Mpileup files can to be very large because they describe each covered base position in the genome on a per read basis, so it is not desired to store them.
For documentation and manuals visit our github.io page.
MpileupToVcf is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of a pipeline, for example the SASC team's biowdl pipelines.