Dindel stage4

[Lien]

Hi all,

I'm trying to detect indels from Exome capture paired-end reads from Illumina.
I aligned my data with BWA and succesfully performed the 3 first stages of the Dindel-program (version 1.01). However, in step 4, I'm somewhat confused: do you first have to merge all files generated in stage 3 into one single file? And is this simply done by 'concatening'?

When I tried without concatenating, I get several errors:
./mergeOutputDiploid.py --inputFiles sample.dindel_stage2_output_windows.txt --outputFile variantCalls.VCF --ref hg19.fa
An error occurred!
Traceback (most recent call last):
File "./mergeOutputDiploid.py", line 351, in <module>
main(sys.argv[1:])
File "./mergeOutputDiploid.py", line 346, in main
mergeOutput(glfFilesFile = options.inputFiles, sampleID = options.sampleID, maxHPLen = options.maxHPLen, refFile = options.refFile, vcfFile = options.outputFile, filterQual = int(options.filterQual))
File "./mergeOutputDiploid.py", line 254, in mergeOutput
fg = open(glfFilesFile,'r')
IOError: [Errno 2] No such file or directory: 'LNCaP_gelukt_BWA.dindel_stage2_output_windows.txt'

When I concatenated a few files into one single file, I still received an error:
./mergeOutputDiploid.py --inputFiles sample.dindel_stage2_outputfiles2.txt --outputFile variantCalls.VCF --ref hg19.fa
WARNING: additional columns in line 1 of file sample.dindel_stage2_outputfiles2.txt were ignored
File msg does not exist
. Aborting.
An error occurred!


Anyone knows what I'm doing wrong?
Thank a lot!
Lien

[skblazer]

I wrote absolute path of all window files from last stage in a text file as --inputFiles,

/your/path/xxxxwindow1.txt
/your/path/xxxxwindow2.txt
/your/path/xxxxwindow3.txt
....

That will work.

[Lien]

Oh, I interpreted it wrong, I thought they meant the content of those files.

It works fine now.
Thanks!

[fitzgeraldlm]

Dindel Stage 4 problems

Hi,

I'm having similar problems to Lien, however mine are unfortunately not solved yet I'm not sure if I understand your solution skblazer or the original instructions (very new to unix/linux).

Currently I am typing in all of the x.dindel_stage2_output files after --inputFiles. So for example if I have three output files I would type

python mergeOutputDiploid.py --inputFiles x.dindel_stage2_output.1.glf.txt x.dindel_stage2_output.2.glf.txt x.dindel_stage2_output.3.glf.txt --outputFile indel.VCF --ref hg18.fa

I get the same message as Lien did when:
WARNING: additional columns in line 1 of file x.dindel_stage2_output.1.glf.txt were ignored
File msg does not exist
. Aborting.
An error occurred!

I tried putting in the whole path name before each sample file thinking that was what you were suggesting skblazer, but it came back with the same message. Have I missed something? Am I supposed to combine all 3 files together beforehand? Is this what you are saying skblazer?

thanks!

[skblazer]

You need create a file, for example "files.txt".
In this file, you should write the following lines:
/your/path/x.dindel_stage2_output.1.glf.txt
/your/path/x.dindel_stage2_output.2.glf.txt
/your/path/x.dindel_stage2_output.3.glf.txt

Then you type the command:
python mergeOutputDiploid.py --inputFiles files.txt --outputFile indel.VCF --ref hg18.fa

That'll work.

Hi,

I'm having similar problems to Lien, however mine are unfortunately not solved yet I'm not sure if I understand your solution skblazer or the original instructions (very new to unix/linux).

Currently I am typing in all of the x.dindel_stage2_output files after --inputFiles. So for example if I have three output files I would type

python mergeOutputDiploid.py --inputFiles x.dindel_stage2_output.1.glf.txt x.dindel_stage2_output.2.glf.txt x.dindel_stage2_output.3.glf.txt --outputFile indel.VCF --ref hg18.fa

I get the same message as Lien did when:
WARNING: additional columns in line 1 of file x.dindel_stage2_output.1.glf.txt were ignored
File msg does not exist
. Aborting.
An error occurred!

I tried putting in the whole path name before each sample file thinking that was what you were suggesting skblazer, but it came back with the same message. Have I missed something? Am I supposed to combine all 3 files together beforehand? Is this what you are saying skblazer?

thanks!

[gaffa]

fitzgeraldlm,

The argument to --inputFiles should be the name of a single text file, this text file in turn containing all the names of the output files. So if your example, you would create a new file with the following content:

x.dindel_stage2_output.1.glf.txt
x.dindel_stage2_output.2.glf.txt
x.dindel_stage2_output.3.glf.txt

That is, the literal names of the output files (you don't need absolute paths). Presumably the rationale behind this is that some runs can generate a very large number of output files, and so it would get difficult to specify them all on the command line. So instead you write all the file names to a text-file, and then the Dindel script looks into this text file. You can generate the text file either manually if you have a small number of output files or by a command like ls | grep ".glf.txt" > list_of_output_files.txt or similar (and then you'd specify --inputFiles list_of_output_files.txt)

EDIT: beaten by skblazer ;]

[fitzgeraldlm]

Solved

A big thank you to gaffa and skblazer. I have now got Stage 4 running and have a VCF file! Thanks for the tip on how to create the txt file gaffa. I did have to add the whole path name, like you suggested skblazer. This may have something to do with the way I installed (or didn't correctly install) Dindel.

Thanks!

[ndiaye]

Hi I am still facing a similar problem:
I've successfully went through first three stages of dindel variant calling, but getting the following error message when using mergeOutputPooled.py to generate the final vcf file. Note that cases_A.gene.ABCA1.glf.txt contain the name of my 10 glf.txt files.
Thank you for helping me to fix that.

[ndiayea@topaz] /shares/data/illumina_datastore/MI_20100215/analyses/Indels_calling/BAM_files/vcf_cases $ python /shares/home/ndiayea/programs/dindel-1.01-python/mergeOutputPooled.py --inputFiles ABCA1_cases_outputfiles.txt --outputFile ABCA1_cases_variantCalls.VCF --ref /shares/data/genome_datastore/homo_sapiens/Homo_sapiens_assembly18.fasta --numSamples 500 --numBamFiles 10
Reading cases_A.gene.ABCA1.glf.txt
An error occurred!
Traceback (most recent call last):
File "/shares/home/ndiayea/programs/dindel-1.01-python/mergeOutputPooled.py", line 620, in ?
main(sys.argv[1:])
File "/shares/home/ndiayea/programs/dindel-1.01-python/mergeOutputPooled.py", line 613, in main
processPooledGLFFiles(glfFilesFile = options.inputFiles, maxHPLen = options.maxHPLen, refFile = options.refFile, outputVCFFile = options.outputFile, doNotFilterOnFR = (not options.filterFR), filterQual = int(options.filterQual), numSamples = int(options.numSamples), numBamFiles = int(options.numBAMFiles))
File "/shares/home/ndiayea/programs/dindel-1.01-python/mergeOutputPooled.py", line 336, in processPooledGLFFiles
raise NameError('Inconsistent glf files! Is the number of BAM files correctly specified?')
NameError: Inconsistent glf files! Is the number of BAM files correctly specified?

[clarissaboschi]

I am having the same problem but I am using the option for pooled samples, I am not sure what to put in the numSamples, is the number of samples/individuals in one of my bam files?
In the outputFiles.txt I have the list of my 78 files.

my command line is
./dindel-1.01-linux-64bit mergeOutputPooled.py --inputFiles outputFiles.txt --outputFile variantCalls_hy7.VCF --ref chick.fa --numSamples 50 --numBamFiles 1

The error message was only
Error parsing input options

But I think my options are correct, what could be the problem?

Thanks

[clarissaboschi]

I solved my problem to run the stage 4, the input file (unique text file) should have the same name as the other files.

I am using numSamples of 10, this is the number of individuals in my pool, but there is no explanation in the manual about it.

But now I am having a vcf file empty, and of course I dont know what is the problem. Anyway the Dindel software is so difficult to run, there are so many steps!