3 posts
For germline variant calling, 30x is sufficient and 100x adds little. Deep coverage pays off for mosaicism, mitochondrial heteroplasmy, structural variants, and cell-free DNA. Here is how to tell which case you are in, and what to check in your own BAM.
A practical answer to RNA-seq depth: 30-40 million paired-end reads for whole-blood expression profiling, why the number moves with your question, and how to check that you got what you paid for.
Read depth in RNA-seq is the number of reads assigned to your sample and, per gene, the number of reads supporting each transcript. This page explains how to compute it from your own files, why 30x means nothing here, and what depth to ask for.