How to generate vcf simply for a single bam file

[mjafin]

Hi there,
Thanks for the brilliant work on rnaseqmut! Been trying to call variants on a single BAM file and I get a tab delimited file in the output, so step 1 working fine. However, when I pass this text file to filtermut.py I get nothing in the output. Have you got any guidelines on how to simply produce vcf files from rnaseqmut? Are you planning on adding any of the fields usually coming from tools such as FreeBayes and Gatk, like AD and DP etc.?

Much appreciated,
Thanks,
Miika