DINDEL --varFile not specified

[jorge]

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

[Heisman]

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:

/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?

[jorge]

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

[Heisman]

Nope, I'm using Dindel 1.01.

[jorge]

Hi Heisman,

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

Jorge

[Heisman]

Ah, yes, I had a problem when I first tried to install it because I used boost 1.48 instead of boost 1.45.