Hi All,
I've successfully went through first three stages of dindel variant calling, but getting the following error message when using mergeOutputDiploid.py to produce the final vcf file.
normal.targets.list is a txt file containing the filenames for all Stage 2 (*.glf.txt) outputs.
Could anyone help out?
Michal
michalkc@stilton:/work/Michal/Finals/2005.2097/Stage2_Normal$ python /usr/local/genetics/dindel-1.01-python/mergeOutputDiploid.py --inputFiles /work/Michal/Finals/2005.2097/Stage2_Normal/normal.targets.list --outputFile /work/Michal/Finals/2005.2097/normal.vcf --ref /work/Michal/Reference_Indexed/Human36.fa
An error occurred!
Traceback (most recent call last):
File "/usr/local/genetics/dindel-1.01-python/mergeOutputDiploid.py", line 351, in <module>
main(sys.argv[1:])
File "/usr/local/genetics/dindel-1.01-python/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 "/usr/local/genetics/dindel-1.01-python/mergeOutputDiploid.py", line 264, in mergeOutput
fn = dat[0]
IndexError: list index out of range
I've successfully went through first three stages of dindel variant calling, but getting the following error message when using mergeOutputDiploid.py to produce the final vcf file.
normal.targets.list is a txt file containing the filenames for all Stage 2 (*.glf.txt) outputs.
Could anyone help out?
Michal
michalkc@stilton:/work/Michal/Finals/2005.2097/Stage2_Normal$ python /usr/local/genetics/dindel-1.01-python/mergeOutputDiploid.py --inputFiles /work/Michal/Finals/2005.2097/Stage2_Normal/normal.targets.list --outputFile /work/Michal/Finals/2005.2097/normal.vcf --ref /work/Michal/Reference_Indexed/Human36.fa
An error occurred!
Traceback (most recent call last):
File "/usr/local/genetics/dindel-1.01-python/mergeOutputDiploid.py", line 351, in <module>
main(sys.argv[1:])
File "/usr/local/genetics/dindel-1.01-python/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 "/usr/local/genetics/dindel-1.01-python/mergeOutputDiploid.py", line 264, in mergeOutput
fn = dat[0]
IndexError: list index out of range