Question regarding use of MAVIS

[oalavijeh]

Dear MAVIS team,

I have a series of strcutural VCFs for 1000 patients with a disease and 17,000 controls. Manta/Canvas have been used to call SVs and each patients SV.VCF is a combination of these two algorithm's calls in a single file.

Would MAVIS be able to accept these as inputs for annotation? I was slightly unclear from your documentation if MAVIS could only be run from the start of a pipeline or if VCFs could be fed into it directly.

Many thanks for your time and I look forward to your reply

Omid

[creisle]

Hi @oalavijeh! Yes you can use any VCF so long as it follows a common pattern of how it stores the structural variant information. VCFs weren't designed with structural variants in mind and as such there tends to be a lot of variation in how people fit them into the specification.

VCFs go into the MAVIS pipeline like any other tool output, they are put into the converter and then whichever parts of the pipeline you would like to run can be done after.

http://mavis.bcgsc.ca/docs/latest/supported_dependencies.html#general-vcf-inputs

>>> mavis convert -h
usage: mavis convert [-h] [-v] [--log LOG] [--log_level {INFO,DEBUG}]
                     --file_type
                     {breakdancer,breakseq,chimerascan,cnvnator,defuse,delly,manta,mavis,pindel,starfusion,strelka,transabyss,vcf}
                     [--strand_specific {True,False}]
                     [--assume_no_untemplated {True,False}] --outputfile
                     FILEPATH -n FILEPATH [FILEPATH ...]

required arguments:
  --file_type {breakdancer,breakseq,chimerascan,cnvnator,defuse,delly,manta,mavis,pindel,starfusion,strelka,transabyss,vcf}
                        Indicates the input file type to be parsed
  --outputfile FILEPATH, -o FILEPATH
                        path to the outputfile
  -n FILEPATH [FILEPATH ...], --inputs FILEPATH [FILEPATH ...]
                        path to the input files

As you can see from the help message for the convert step it accepts a vcf as input (instead of a specific tool).

Try this out and if you have any questions or issues let me know! if the output is non-standard and will not work as general vcf input feel free to make a ticket requesting processing this input as a feature

[creisle]

Closing for lack of activity