soft-clipping during alignment and variant calling query

Question

[prasundutta87]

It is known that BWA-MEM soft-clips bases to achieve a higher alignment rate. If a variant caller is used after that, say, GATK Haplotyecaller, is it necessary to keep the parameter --dont-use-soft-clipped-bases to TRUE? Or should we keep it in default (false) as it may affect the realignment step during Haplotycaller run?

[WouterDeCoster]

Please stick to the GATK best practices. If they don't recommend to use that parameter there is no need to overthink.