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Old 03-04-2011, 12:40 AM   #1
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Join Date: Sep 2010
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Default GATK calling Merged Bam files

Dear All,

can share your idea? i have tried to merge my bam files (bam file1, bam on) using samtools and picard. After then, i used GATK to call the SNP and refer to the merged bam file. However, the GATK always throw out genotyp results with 2 columns or more pertaining to my number of bam files prior the merging instead of a single column result for the merged bam file.

Any idea?anyone can share the experience?many thanks in advance...

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