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Old 02-03-2011, 10:59 AM   #3
fitzgeraldlm
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Location: Seattle

Join Date: Jan 2011
Posts: 4
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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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