Soft clips are segments of reads that are marked by the mapper (in this case BWA) as being not useful, so they are hidden by default by IGV. The mapper introduces soft clips in the CIGAR string of a read when it encounters bases, typically toward the end of the read, that it is not able to align to the reference to its satisfaction based on the scoring model it employs. At some point, the mapper gives up trying to align the bases, and just puts in the S operator to signify that downstream tools should disregard the following bases, even though they are still present in the read record. Some mappers even remove those bases, which is called hard clipping, and uses the H operator instead of S.Soft clips are interesting to us because they often occur in the vicinity of insertions, especially large insertions.
《Genomics in the cloud》

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