Dindel --outputRealignedBAM

fitzgeraldlm · 01-20-2011, 04:04 PM

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.

libiyagirl · 02-03-2011, 11:35 AM

I have the same question. Any idea?

fitzgeraldlm · 02-03-2011, 11:59 AM

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.

libiyagirl · 02-04-2011, 07:33 AM

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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01-20-2011, 04:04 PM	#1
fitzgeraldlm Junior Member Location: Seattle Join Date: Jan 2011 Posts: 4	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.

02-03-2011, 11:35 AM	#2
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	I have the same question. Any idea?

02-03-2011, 11:59 AM	#3
fitzgeraldlm Junior Member Location: Seattle Join Date: Jan 2011 Posts: 4	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.

02-04-2011, 07:33 AM	#4
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	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.