Hi,
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?
Cheers:
Szilva
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?
Cheers:
Szilva