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111 bytes added ,  14:31, 8 February 2012
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   bin/samtools index bams/$file.bam
 
   bin/samtools index bams/$file.bam
 
   end
 
   end
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 +
 +
Once we finish the read mapping step and generate bam files for all samples, we can step to variant calling.
    
== Calling variants and Inferring genotypes ==
 
== Calling variants and Inferring genotypes ==
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