Hi All,
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?
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?
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