BED file for targeted sequencing

[ycl6]

I saw in #7 that for amplicon-awared variant calling, the BED file need to have 8 columns storing both the primer and insert positions. However, the BED file that comes with the manufacturer's targeted capture bed contains only a set of positions. Is there a recommended strategy in creating a BED file suitable for VarDict to perform variant calling?

Given that I don't have the primer information, what's the appropriate -M INT setting for a typical targeted sequencing experiment?

[mjafin]

Hi @ycl6 and thanks for your interest in using VarDict. Is your data from a PCR amplicon run? Ideally you'd get the primer bed file from the PCR amplicon vendor. Otherwise you'd probably just have to run VarDict with a 3 column bed file and not in amplicon-aware mode.

As to the -M option I'd refer you to @zhongwulai