Chapter 10

Genomics and Variants

• ChIP-seq

  A ChIP-seq peak file always looks like an answer, so the real skill is checking it against biology you already know before you believe it.

• FRiP (fraction of reads in peaks)

  A single number that tells you whether your ChIP-seq or ATAC-seq depth landed on real signal or was wasted on background.

• Germline vs somatic variants

  The label you assign a variant decides whether it goes in a genetic counseling report or a tumor board slide, and VAF alone won't tell you which.

• Peak calling

  The MACS2 output you trust without checking known biology is the fastest way to publish noise as a binding site.

• Variant calling

  The step where a coordinate-sorted BAM becomes a VCF of real mutations, if you know which artifacts a caller can't tell from truth.