Im getting the following output when trying to run all2vcf stats on my vcf files.
[Wed Jun 29 10:59:38 2022] ### Working on pairs/indels/vcfs/Scaffold_8.Scaffold_17.vcf ###
[Wed Jun 29 10:59:38 2022] Found 883 candidate indels that where the annotation did not comply the VCF standard
[Wed Jun 29 10:59:38 2022] The annotation was fixed for these 883 indels
[Wed Jun 29 10:59:38 2022] Extracting information on the retained variants ... Traceback (most recent call last):
File "/home/mike/software/all2vcf/src/stats", line 197, in <module>
stats["INFO"] = stats["INFO"].str.split(";").apply(lambda x:convert_to_dictionary(x))
File "/home/mike/miniconda3/envs/appraisal/envs/appraisal/lib/python3.9/site-packages/pandas/core/series.py", line 4357, in apply
return SeriesApply(self, func, convert_dtype, args, kwargs).apply()
File "/home/mike/miniconda3/envs/appraisal/envs/appraisal/lib/python3.9/site-packages/pandas/core/apply.py", line 1043, in apply
return self.apply_standard()
File "/home/mike/miniconda3/envs/appraisal/envs/appraisal/lib/python3.9/site-packages/pandas/core/apply.py", line 1098, in apply_standard
mapped = lib.map_infer(
File "pandas/_libs/lib.pyx", line 2859, in pandas._libs.lib.map_infer
File "/home/mike/software/all2vcf/src/stats", line 197, in <lambda>
stats["INFO"] = stats["INFO"].str.split(";").apply(lambda x:convert_to_dictionary(x))
File "/home/mike/software/all2vcf/src/stats", line 71, in convert_to_dictionary
dict = { x[0]:x[1] for x in dict }
File "/home/mike/software/all2vcf/src/stats", line 71, in <dictcomp>
dict = { x[0]:x[1] for x in dict }
IndexError: list index out of range
The vcfs are called from a converted mummer show-snps output, of a nucmer alignment between two assembly contigs.
Hi,
Im getting the following output when trying to run all2vcf stats on my vcf files.
The vcfs are called from a converted mummer
show-snps
output, of a nucmer alignment between two assembly contigs.Any help would be hugely appreciated. Thank you.