input bam files refinements

[linsson]

Hi. In some SNP discovery protocols it is suggested to perform pcr duplicate labeling and base quality score recalibration if possible. Would you also recommend this before running dysgu?

As for pcr duplicates, in case, is tagging enough or is removal better?

[kcleal]

Hi @linsson, I recommend duplicate marking - this is standard procedure for most pipelines. Just tagging duplicates is enough - dysgu will ignore reads flagged as duplicate.

[linsson]

Thanks a lot @kcleal !