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Old 01-20-2011, 04:04 PM   #1
fitzgeraldlm
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Default Dindel --outputRealignedBAM

Has anyone tried using the --outputRealignedBAM option in Dindel?

I would like to try using the realigned BAM files Dindel outputs in SAMtools for SNV calling but I can't work out where to use this option. If someone has done this, any (very new-user-friendly) tips on how to do this and also how to put all the Dindel BAM files back together for use in SAMtools would be greatly appreciated!

lmf.
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Old 02-03-2011, 11:35 AM   #2
libiyagirl
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I have the same question. Any idea?
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Old 02-03-2011, 11:59 AM   #3
fitzgeraldlm
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Hi Libiyagirl,

I'm pretty sure you use this command in Stage 3 of Dindel, although I didn't end up trying it. I ended up teaching myself how to use GATK and have successfully done a local realignment using this program. I'm sure you could then use the outputted BAM file that GATK produces in SAMtools at the pileup stage...or just keep working through GATK and the UnifiedGenotyper stages to get your indels and SNVs through that.

LMF.
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Old 02-04-2011, 07:33 AM   #4
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Hi Fitzgeraldlm, thank you very much for the tips! Currently my supervisor wanna me try Dindel first, but I'm sure I will use GATK soon.
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