how do I output the CS tag for BWA align of SOLID reads?

Hi I am trying to use GATK to run some analysis on BWA aligned colorspace reads but I encountered this problem described here http://getsatisfaction.com/gsa/topics/problem_running_recalibration_on_a_solid_bam_file?utm_content=topic_link&utm_medium=email&utm_source=reply_notification

basically "org.broadinstitute.sting.utils.StingException: Unable to find color space information in SOLiD read."

I am aware that BFAST generates this info. How do I make BWA generate this tag as well?

asked 25 Jun '10, 01:46

KevinL
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1	Unfortunately there is no option in BWA. I would try asking the author for this feature. Email bio-bwa-help@lists.sourceforge.net. link answered 25 Jun '10, 12:13 nilshomer 76●4 accept rate: 0% edited 25 Jun '10, 12:13

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Tags:

bwa ×17
samtools ×13
solid ×5
colorspace ×1
tag ×1

Asked: 25 Jun '10, 01:46

Seen: 918 times

Last updated: 25 Jun '10, 12:13

how do I output the CS tag for BWA align of SOLID reads?

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