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  • Marking duplicates and comparing 2 WE samples?

    Hey,

    Two follow-up questions for my WholeExome Analysis:

    1) I used Picard "MarkDuplicates" to mark duplicates and called bam as "marked.bam". I used snpeff to annotate snps and indels etc. The file written using marked.bam is smaller than un-marked bam (~5000 rows smaller). So I am assuming snpeff is not taking into account PCR duplicates. Is this correct?

    2) Now I want to compare snpeff result between two samples. ANy recommendations for softwares for this? I obviously will compare SNP and INDELS etc.

    Thanks very much again.
    Last edited by angerusso; 02-20-2012, 01:45 PM.

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