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Old 01-01-2016, 03:00 PM   #1
Mike_Brown
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Default How to convert BAM file into dosage array data

I am new to bam file. I was using dosage data of genotypes to do association test (each column represent a snp, and each row represent an individual). Is it possible to convert bam file to this kind of file?
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Old 01-01-2016, 03:10 PM   #2
mastal
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You can use the bam files as input to a program that does genotype calling, like GATK, for example.

https://www.broadinstitute.org/gatk/
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