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Differences between BQSR pipeline in two different GATK documents

Hi,

I noticed that the pipeline for BQSR is slightly different between the "Workshop walkthrough (Brussels 2014)" document and the "(howto) Recalibrate base quality scores = run BQSR" document. I used the former document as my guide since it is more recent, but I am curious as to why these two are different. The first step is the same for the 2 docs, but then for the second step, the output is a recal.bam file in the brussels document instead of a post_recal.table file in the (howto) document. Then, I am confused about the (howto) document because it seems that the 4th step is exactly the same as the second step, except we generate a recal.bam file. Is the brussels document presenting steps that are more efficient? (since there is only 1 use of -BQSR to generate the recalibrated bam file we need, as opposed to 2 uses of the option)

Thanks,
Alva

Best Answer

Answers

  • astrandastrand New YorkMember

    OK, thanks for the explanation.

    Alva

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