Accepted input files

The accepted input files to run analyses on VarSome Clinical are either:

  • FASTQ files only from Illumina or MGI sequencers. Files must be compressed and have the .fastq.gz extension.

Paired-end reads must be provided in two different files, e.g.: sample_R1.fastq.gz and sample_R2.fastq.gz.

We expect files that conform to Illumina's naming convention. We can deal with multiple files, but we need the file names of each pair of paired-end files to be the same and only differ in the _N (or _RN).  When parsing names of paired-end read files, we look for "" and "" where foo and bar need to be the same for the two pairs, and the only difference is the number. Alternatively, we also handle "" and "". 

  • VCF files with standards-compliant format, regardless of sequencing platform. There is also support directly for VCF files from IonTorrent platform. Please, check this link to find more details about requirements for submitted VCFs.