Thread: SNP calling
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Old 12-19-2012, 03:49 PM   #7
Zam
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Location: Oxford

Join Date: Apr 2010
Posts: 51
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Cortex is designed to call variants between samples, without a reference.

Papers:
1. De novo assembly and genotyping of variants using colored de Bruijn graphs.
Z Iqbal, M Caccamo, I Turner, P Flicek, G McVean, Nature Genetics (2012)

2. High-throughput microbial population genomics using the Cortex variation assembler. Z Iqbal, I Turner, G McVean, Bioinformatics 2012

Software freely available here:
http://cortexassembler.sourceforge.n...ortex_var.html

Manual here
http://cortexassembler.sourceforge.n...ser_manual.pdf

It can take BAM or fast files as input. Hope that helps!

Zam
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