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  • skblazer
    Member
    • Feb 2009
    • 51
    #1

    Calling SNPs and InDels simultaneously or seperately?

    Hi,

    I want to know when call variants by GATK pipeline, you call SNPs and InDels simultaneously (use -glm BOTH) or separately in two rounds of run. I noticed that considering BAQ will decrease the performance of calling InDels. But how can I deal with the conflicted alleles generated by SNPs and their nearby InDels?

    Best,
    SK
    Tags: indel snp
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