Dindel

[zhangtao13039]

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 !!!!!

[gaffa]

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?

[zhangtao13039]

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!!

[dk003m]

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