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Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.2 (i.e. the second beta release) is out. See the GATK4 BETA page for download and details.

Removing duplicates and replicates before or after local realignment and bqsr

songchunsongchun Peking, ChinaMember

We've called variants from our own exome data sets. When compaired with the protocol of 1000 genomes, we found that they just marked duplicates and replicates after local realignment and bqsr rather than removing them before, which is the case of ours. Since we wanna use the CHB and CHS as controls, will the distinct calling strategy affect the final output a lot?

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  • songchunsongchun Peking, ChinaMember

    Got it. What's the advantage of doing local realignment before marking duplicates, as in our exome data? If so, do we have to recall the variants following the protocol of 1000 genomes?

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