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Old 10-10-2012, 05:05 AM   #3
rahilsethi
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Location: Pittsburgh, PA

Join Date: May 2010
Posts: 22
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Hi nilshomer,

Thanks for the suggestion. Although SHRiMP, in general, does not give any separate option for .qual files in the run, I did try to incorporate qual files along with csfasta; but it prompts and error, indicating that it does not recognize the .qual format.
One suggestion has been recommended to me by SNVer authors is to include a dummy value in QUAL field of SHRiMP SAM output such as "IIIII" (size of SEQ length) for all mapped reads so as to generate variant calls without runtime error. But then, that would affect the filter process of the variants.
I have also come across the variant calling tool VARiD that shows an example of working on SHRiMP mapping output. I might give a try to VARiD. Do you know how good is VARiD tool for variant calling?
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