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ATLAS / Auxiliary Tools: assessSoftClipping


This tool provides soft clipping statistics for all reads, i.e. the number of soft-clipped positions and their bases.


a txt file with suffix _clippingStats.txt.gz with the following information:

  • read name
  • mapping position of read
  • number of softclipped bases on the left side of the read
  • number of bases that were not softclipped per read
  • number of softclipped bases on the right side of the read

if the option printSequences is used, the sequences underlying these statistics are also written to file.

Usage Example

./atlas task=assessSoftClipping bam=example.bam printSequences

Specific Arguments

  • printAll: Write softclipping stats for all alignments to file, also those that do not have any softclipping
  • printSequences: Write softclipped sequences to file

Engine Parameters

Engine parameters that are common to all tasks can be found here.