Depending on the source data, VarSome Clinical charges either per number of megabases in reads or per number of variants, in the FASTQ or VCF single sample, respectively.
Starting from FASTQ
When starting analysis from FASTQ, VarSome Clinical charges per number of bases in reads per sample. The size of the region of interest is not the defining factor. What VarSome Clinical cares about, and what you can see in the pricing sheet, is the number of bases (nucleotides) in the input FASTQ file.
For example, if you have done a run of 50 clinical exomes and have read output of 120 gigabases (Gb; Maximum Output for NextSeq, as specified in the machine technical documentation), then each exome sample contains 120 / 50 = 2.4 Gb in reads, which is equal to 2,400 megabases (Mb). To get the price, take this number and consult the pricing sheet.
Another way to look at it is as follows:
- Region of Interest for Clinical Exome: 20 Mb
- Region of Interest for Whole Exome: 60 Mb
So if you sequence a clinical exome of 20 Mb, the average coverage is 100x and the 90% of reads align, the number of bases in reads is 20 x 100 / 90% = 2,222 Mb. To get the price, take this number and consult the pricing sheet.
Starting from VCF
Starting from VCF, VarSome Clinical charges per number of variants in the VCF file. You may upload a multi-sample VCF, which will be automatically broken into individual samples, and charged accordingly on the per-sample basis.