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Old 01-23-2012, 03:01 AM   #1
jorge
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Location: Madrid, Spain

Join Date: Jun 2011
Posts: 25
Default DINDEL --varFile not specified

Hello,

I'm aware this issue (or similar) has been alerady posted but I don't get DINDEL to work for the 'Stage 3' (version 1.0, page 4 of the documentation). Basically it asks me for the candiate variant file ('Please specify the file with the candidate variants.'). However I think I've already supplied the windows file using the following command where '--varFile' is used for that.

[PATH_TO_DINDEL]/dindel \
--analysis indels \
--doDiploid \
--bamFile [PATH_TO_BAM_FILE]/file.bam \
--ref [PATH_TO_REFERENCE_GENOME]/hg19.fa \
--varFile [PATH_TO_CANDIDATE_VARIANTS_FILE]/file.windows.1.txt \
--libFile [PATH_TO_LIBRARY_FILE]/file.libraries.txt \
--outputFile [PATH_FOR_OUTPUT_FILE]

I would d be grateful if someone could help me to identify what I'm dowing wrong.

Thanks a lot
Jorge
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Old 01-23-2012, 05:03 AM   #2
Heisman
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Posts: 535
Default

I love Dindel, but it was a big hassle to figure out how to make it run.

I wrote a bash script to run Dindel as part of a larger pipeline. I have tried to take out the relevant lines and delete things that are not necessary. Hopefully it can help you and others out:

Code:
/dindel-1.01-src/dindel --analysis getCIGARindels --quiet --bamFile [aligned_file] --outputFile [dindel_output_1] --ref [reference.fa]

mkdir [first_directory]

/dindel-1.01-python/makeWindows.py --inputVarFile [dindel_output_1].variants.txt --windowFilePrefix [first_directory/temp_one] --numWindowsPerFile 1000

mkdir [second_directory]

trial=`ls -1 [first_directory] | wc -l`

for ((i=1;i<=trial;++i))

do

/dindel-1.01-src/dindel --analysis indels --doDiploid --quiet --bamFile [aligned_file] --ref [reference.fa] --varFile [first_directory/temp_one].'$i'.txt' --libFile '[dindel_output_1].libraries.txt' --outputFile '[second_directory].dindel_output_stage1_output_windows.'$i

done

ls [second_directory] | grep ".glf.txt" > [dindel_list]

sed 's,^,[second_directory]/,' [dindel_list] > [full_dindel_list]

/Users/blevinson/Shared/DINDEL/dindel-1.01-python/mergeOutputDiploid.py --inputFiles [full_dindel_list] --outputFile [dindel_variant.vcf] --ref [reference.fa]
In your case I can't see anything obviously wrong... are you 100% sure you have the path correctly specified?
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Old 01-23-2012, 05:54 AM   #3
jorge
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Default

Hello Heisman,

Thanks for the code. Just one question, are you using dindel-0.12 ? I that case I get the program to work, however I get the error if I use dindel-1.01.

Thanks
Jorge
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Old 01-23-2012, 06:07 AM   #4
Heisman
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Nope, I'm using Dindel 1.01.
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Old 01-23-2012, 06:12 AM   #5
jorge
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Hi Heisman,

Ok thanks, I got feedback from Kees (the author). It seems it's a problem with my boost version.

Jorge
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Old 01-23-2012, 06:13 AM   #6
Heisman
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Ah, yes, I had a problem when I first tried to install it because I used boost 1.48 instead of boost 1.45.
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