Hi all,

I sequenced dozens of genes in tumor-normal samples using truseq custom amplicon kit on Miseq (with average depth ~1000x）. But if I process the data using the somatic variant caller which used in MiSeq's Amplicon Workflow,the results seem to be too rough,and I have no idea to find out the possible germline or somatic mutations.

Anyone has any idea about the pipeline of analysis? And what is the general standard for germline/somatic mutation.

Thanks.