Skip to content

Soft clipping

Definition
AI-generated

Soft clipping retains a read’s full sequence in the SAM/BAM record but excludes clipped bases from alignment coordinates, often when only a prefix or suffix aligns cleanly.

Topics
Sequencing Data Analysis
Related
Chimeric read Hard clipping Read mapping

Why it matters in GWAS

Soft clips flag adapter contamination, poor tails, or local misassembly near indels; excessive clipping can indicate mapping problems.

Example usage

"Soft clipping was tallied per site to prioritize structural-variant breakpoint inspection."

Chimeric read Hard clipping Read mapping
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Li H, et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics.
← Single Nucleotide Variant (SNV) Software Thread →

Last updated (UTC · Git history)