While testing ScanNeo on some mouse data, I get the following error. I have a patch that I will submit shortly that fixes this issue.
$ ScanNeo.py indel -i ../variant_calling_work/CRO030321_001.noDups.bam -r mm39
Checking for 'picard': found /mnt/store3/clustcrilab/tools/scanneo/miniconda/bin/picard
Checking for 'vep': found /mnt/store3/clustcrilab/tools/scanneo/miniconda/bin/vep
Checking for 'sambamba': found /mnt/store3/clustcrilab/tools/scanneo/miniconda/bin/sambamba
Checking for 'bedtools': found /mnt/store3/clustcrilab/tools/scanneo/miniconda/bin/bedtools
Checking for 'bwa': found /mnt/store3/clustcrilab/tools/scanneo/miniconda/bin/bwa
Checking for 'transIndel_build_RNA.py': found /mnt/store3/clustcrilab/tools/scanneo/bin/transIndel_build_RNA.py
Checking for 'transIndel_call.py': found /mnt/store3/clustcrilab/tools/scanneo/bin/transIndel_call.py
Traceback (most recent call last):
File "/mnt/store3/clustcrilab/tools/scanneo/bin/ScanNeo.py", line 987, in <module>
main()
File "/mnt/store3/clustcrilab/tools/scanneo/bin/ScanNeo.py", line 899, in main
bwa_bam = preprocessing(args.input, ref=args.ref)
File "/mnt/store3/clustcrilab/tools/scanneo/bin/ScanNeo.py", line 163, in preprocessing
fasta = config["mm39_ref"]
KeyError: 'mm39_ref'
While testing ScanNeo on some mouse data, I get the following error. I have a patch that I will submit shortly that fixes this issue.