simple , somatic ,amplicon mode

[kkamii]

hello!

I read your guideline and followed it using my bam file. But, I don't understand the difference among simple mode, somatic mode, amplicon mode.

Could you explain the difference briefly??

thank you :)

[jasteen]

Whilst i'm not a dev, I have used vardict a lot.

simple mode is single sample mode. ie, not somatic pairs. Single germline or unmatched tumor samples.

somatic mode is exactly as it suggests. matched germline/tumor pairs for calling somatic variants.

amplicon mode is for amplicon based panel sequencing. Where there are a lot of reads that share the same start and stop coordinates.

[kkamii]

Thank you !!

[PolinaBevad]

Thanks a lot Jason (@jasteen) for answering this! @kkamii thank you for using VarDict! I'll close the issue!