Tagged with #targetcoverageefficiency
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Created 2012-07-23 23:56:59 | Updated 2012-07-23 23:56:59 | Tags: targetcoverageefficiency gatkdocs
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A new tool has been released!

Check out the documentation at TargetCoverageEfficiency.

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Created 2015-01-12 10:10:49 | Updated 2015-01-12 10:56:11 | Tags: targetcoverageefficiency multi-sample variant-calling merge-bam
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Hi, I have with me 1000 samples that were pooled together in 5 different libraries and sequenced for genomic regions. So first, for each library, I independantly performed alignment, marked duplicates,realigned the bam files and also did recalibration and separated the bam file for each individual. Now I have 1000 individual bam files and I wanted to check the target coverage and perform variant calling. I wanted to know if it makes sense to merge the bam files according to cases:controls and perform the analysis with 2 bam files or is it better to carry on with single individual bam files ?

Many thanks.