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Old 08-06-2012, 12:42 AM   #3
shyam_la
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Location: California

Join Date: Mar 2012
Posts: 97
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It appears you have used MuTect to call your SNVs. The current beta version of MuTect is very verbose and the initial output is more than a hundred fold bigger than it should be.

use "grep -v REJECT variant_file > variant_file_KEEP" to get the real variants and then annotate.
You may also want to remove "UNCOVERED" variants and "DBSNP" variants.. The example variant you have given is a total failure..
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