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08-20-2011, 06:17 AM
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#1 |
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Junior Member
Location: china Join Date: Aug 2011
Posts: 4
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Dindel
hello ,recently,i have used the Dindel 1.01,but in the stage1,the stage1_dindel.variants.txt is empty!!!!
i don't kown how to solve the problem..bam and bam.bai ;fa and fa.fai are exists!!! i haven puzzled for a long time,wish someone can help me !!!!! 
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08-20-2011, 01:20 PM
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#2 |
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Member
Location: Gothenburg/Uppsala, Sweden Join Date: Oct 2010
Posts: 82
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What is the exact command that you used, and do you get any error or diagnostic messages? Also what about the libraries.txt file, is it also empty?
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08-20-2011, 07:11 PM
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#3 |
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Junior Member
Location: china Join Date: Aug 2011
Posts: 4
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sorry,only the stage1_dindel.variants.txt is empty.
my command is like this :./dindel-1.01-linux-64bit --analysis getCIGARindels --bamFile ./500.bam --outputFile stage1.Dindel --ref ./fa the fa.fai and bam.bai are exists!! for no error massege so i don't know what is the matter!! |
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12-01-2011, 11:34 AM
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#4 |
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Junior Member
Location: Los Angeles Join Date: Dec 2011
Posts: 2
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try indexing both the reference and bam file with the latest samtools.
I had the same problem because I generated the index files using some other program and tried running it and I got empty an empty file too. But after indexing with samtools it worked. hope that helps |
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