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# Removing duplicates and replicates before or after local realignment and bqsr

Peking, ChinaMember Posts: 2

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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