dindel: stage 4 crach

[michalkovac]

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