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Old 02-10-2011, 08:09 AM   #1
Location: Hungary

Join Date: Aug 2009
Posts: 16
Default CS and CQ in Bowtie output for GATK


I have SOLiD reads and I am using GATK for variant call and Bowtie for alignment. Is there a way to force Bowtie to write out the color reads and qualities ( the CS and CQ tags in SAM) as GATK is expecting these?

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