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Old 06-24-2012, 01:13 AM   #1
Applemelon
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Location: China

Join Date: Jun 2012
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Default About the Recalibration of Best Practice Variant Detection with GATK v3

I tried to follow the protocol of"Better: sample level realignment with known indels and recalibration" in "Best Practice Variant Detection with GATK v3".

It said to recalibrate the realigned bam. And it seems that I should provide a database of known polymorphic sites before I can run CountCovariates of GATK. I wondered,

1, if I had not such a database in hand, should I use my resequencing data to create the database from scratch? How does the quality play roles on SNP or polymorhism ? Should I use the recalibrated bams to call polymorphism sites again?

2, if there is a database from other project, should I combine the polymorphic sites from my data with it?

Thank you.
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