SEQanswers (
-   Bioinformatics (
-   -   Ask for help! GATK iteration~ (

wzhangvv 05-27-2013 07:36 AM

Ask for help! GATK iteration~
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!


All times are GMT -8. The time now is 11:26 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.