Using Lastl I aligned a filtered fastq of mutant DNA to fasta of a reference chromosome. The alignment of the output is currently in a maf format and is EXTREMELY huge.... something like 35.7 GB. I would now like to generate a VCF file for indels and snps, but am not sure which tool is best for this.
There are several line command tools to convert MAF to VCF format, but none are wrapped for Galaxy yet (or at least not publically shared in the Main Tool Shed). If curious about using the line-command choices, please review Q&A at https://www.biostars.org or just google with "maf to vcf" (or similar) to locate options.
Once you have a vcf file, that can be uploaded to Galaxy and used with the data manipulation/annotation tools that accept that input format.
If anyone else knows of a tool for this function that is already wrapped for Galaxy, please reply to this post. Or should someone be interested in wrapping a tool (existing or new), it would be welcome in the Tool Shed!
Thanks! Jen, Galaxy team