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Old 01-05-2011, 03:22 AM   #1
ketan_bnf
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Location: India

Join Date: Oct 2010
Posts: 59
Default Exome sequence annotation

Hi!

I am doing Exome annotation, for that pipeline is,

I have 454 sequencing data, so i am planning to use MOSAIK for aligning reads to ref. chromosome and then extract data from aligned_sorted file to BAM/SAM format, going to analyze with samtools.

Is this the right pipeline for Exome annotation SNP finding of 454 data?
Does bwa supports reads (40-616 length) of 454 seq data? can it handle that?

Thanks,
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Old 01-06-2011, 01:21 PM   #2
ntremblay
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Default

Hi,

have a look at this tool, it works perfectly from samtools pileup and you can choose to annotate variation according to many dataset (snp131, 1000g, etc.). Also, the website is well documented on how to install and use the program.

http://www.openbioinformatics.org/annovar/

Hope that helps,

Nicolas
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