SNP annotation in snpeff using custom motif database

Question

[johntlovell]

Hi all, I am working with a non-model system to annotate SNPs. I have used snpeff successfully to annotate the basic features (coding, intron, etc.) but I also want to annotate transcription factor binding motifs. I have a pwms motif database from Jaspar and want to supply this to the -motif option in snpeff.

While it is clear how to do this with mouse and human (via publically available databases), it is not obvious how to generate a motif.bin file and supply this to snpeff.

Any advice is much appreciated.

John