User:Jarle Pahr/GATK
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Notes on the Genome Analysis Tool Kit (GATK):
http://www.broadinstitute.org/gatk/
http://seqanswers.com/wiki/GATK
GATK Best Practices: http://www.broadinstitute.org/gatk/guide/topic?name=best-practices
Picard:
https://www.broadinstitute.org/files/shared/mpg/plathumgen/plathumgen_fennell.pdf