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  • YKay
    Junior Member
    • Jun 2010
    • 3
    #1

    Batch effect, SNPs

    Dear all,

    has anyone encountered batch effects on SNP calling?

    In my project we made two HiSeq 2000 sequencing rounds (multiple individuals per round), reference mapping by BWA for all the individuals, removal of duplicates and SNP calling by Samtools mpileup. The Principal Component Analysis of the SNPs showed a clustering according to the batch rather than the expected population structure.

    Does anyone have any insight on how this batch effect arised and also any idea on how to remove it?

    Thank you!
    Tags: None
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