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One extra base in reads

sp580sp580 GermanyMember

Hello!
I have a set of fastq files in which all reads have a length of 151bp, but they are supposed to be 150bp.

I checked two threads related to this:
http://seqanswers.com/forums/showthread.php?t=61997
https://www.biostars.org/p/162922/

Apparently it is necessary to remove that base because it is not reliable, but I already did the trimming, alignment and BQSR, following GATK est practices.

Does GATK take such an event into consideration when processing the alignments and calling variants?, should I re-do the steps I have done so far?, how do you guys handle this?

There is a study for example, where the "extra" base (100bp vs 101bp) was kept:
https://www.nature.com/articles/srep14168#results-and-discussion

Thanks!

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