pegi3s/maffilter repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of MafFilter⁠, a multiple genome alignment files processor.

⁠Using the MafFilter image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/maffilter input.file=/data/mafFile input.file.compression=none input.format=Maf output.log=/data/out_name.log "maf.filter=XFullGap(species=(hg18, panTro1, baboon, mm4, rn3)), Output(file=/data/filtered.maf)"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input file(s).
• mafFile to the actual name of your MAF alignment file.
• output/out_name.log to the actual name of your output file.
• XFullGap(...) to the MafFilter filter(s) you want to apply.
• filtered.maf to the actual name of your output file.

To see the MafFilter⁠ help, just run docker run --rm pegi3s/maffilter.