soft-clipping during alignment and variant calling query · Biostar

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soft-clipping during alignment and variant calling query

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?

bwa-mem gatk variant calling alignment

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updated 6.7 years ago by Biostar

• written 6.8 years ago by prasundutta87

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

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written 6.8 years ago by WouterDeCoster

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