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Old 08-25-2011, 05:07 AM   #10
Fabien Campagne
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Location: New York City

Join Date: Feb 2010
Posts: 39
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Quote:
Originally Posted by TuA View Post
Thanks everyone for your suggestions!

The problem is that samtools is the only software (at least that I know of) which provides the 'raw.vcf' format, ie the information for all sequenced sites (not only SNP positions). This format is required to be able to compare data among individuals (population genomics).
You can also call genotypes for all sequences positions with Goby. You will need the 'genotypes' output format of the discover-sequence-variants tool to get all sites sequenced.

See the tutorial at http://campagnelab.org/software/goby...ence-variants/

Note that you can convert BAM alignments to Goby format with the tool sam-to-compact.
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