Wes analysis - Quality control on sequenced data

Question

[AndreaSibi]

Hello everyone,

we are doing a WES analysis experiment in order to follow the variant calling process and we have developed our own pipeline.

Since we want to use GATK's best practices, the question is whether or not it is really necessary to execute the first step of quality control (and possibly trimming if necessary) of the sequenced data? (before alignment)

Thanks for your help.

Answer 1

[JC]

is really necessary to execute the first step of quality control (and possibly trimming if necessary) of the sequenced data?

defnitively yes, in case you get a bad sequencing data, you don't want to spend cpu-time on garbage

[karl.stamm]

If you're sure your data is clean, that's because you or someone else has already performed the quality control step.