Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Advice re multi-lane samples

drchriscoledrchriscole Posts: 16Member
edited January 2013 in Ask the team

Hi,

I have exome data run on two lanes per library is it better to combine the lanes into one or to run each lane independently through GATK? What are the pros and cons? Many thanks

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