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
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
Comment