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Old 08-16-2012, 10:31 AM   #1
Location: Massachusetts

Join Date: Feb 2009
Posts: 50
Default Calling SNPs and InDels simultaneously or seperately?


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?

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indel snp

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