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Old 06-27-2012, 07:36 PM   #1
oiiio
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Default Variation Callers?

I am analyzing some whole genome data and at the moment I use GATK for indels and SNPs. What are some other tools or pipelines out there for whole genome analysis?

For example I read the HugeSeq paper, and I saw pindel, CNVnator, BreakDancer, and BreakSeq. Does anyone have other recommendations or preferences among these ?

And do you (or how do you ) combine results from two programs, such as UnifiedGenotyper and Pindel?
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Old 06-27-2012, 11:28 PM   #2
Jane M
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Hello,

There is the same topic here: http://seqanswers.com/forums/showthread.php?t=15000, in case it helps.

There are also SomaticSniper, MuTect & SNVMix (only for SNPs) and VarScan...
I have not yet any experience in combining results from two programs, so I cannot help, but I am interested in the answer
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Old 06-27-2012, 11:43 PM   #3
Zam
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one more for the long list:

http://seqanswers.com/forums/showthread.php?t=16695
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Old 06-28-2012, 04:59 AM   #4
aeonsim
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Real time genomics (rtg) commercial great for trios
Freebayes
Samtools

Are other good tools.
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Old 06-28-2012, 07:58 AM   #5
oiiio
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Thanks for the replies so far,

I'm extremely interested in the combinations of tools - like HugeSeq's pindel and unified genotyper combo - that people think form really comprehensive analysis?
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Old 02-05-2014, 01:13 AM   #6
dnusol
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Hi there

it seems that FreeBayes has not been published yet. Is this so?

http://arxiv.org/abs/1207.3907


Thanks

Dave
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Old 02-05-2014, 06:45 AM   #7
girlmonkey
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We are using Platypus (http://www.well.ox.ac.uk/platypus) for our Haloplex panels.
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