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-   -   Ask for help! GATK iteration~ (http://seqanswers.com/forums/showthread.php?t=30536)

wzhangvv 05-27-2013 07:36 AM

Ask for help! GATK iteration~
 
Hi,
I recently used several aligners to do the tests for SNPs calling. Without any iteration step, the bowtie2-local-very sensitive performed better than bwa. It could call more real SNPs than both bwa and smalt. But after the iteration steps, bowtie2 only yielded a few SNPs and lost many real ones. With the same default recalibration parameters, SNPs based on bwa alignment were very constant after 5 iterations.
Can you guys help me to figure it out? How can I keep more SNPs based on bowtie2 alignment after iterations?
Thanks in advance!

Wei


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