Hi
I have run DiscoSNP++-v2.2.10 on 20 samples of yeast using on reference to map the results to. I have run it with -k 31 and -P100. Then I want to map the results to another reference using run_VCF_creator.sh.
When I do that I get the error: Traceback (most recent call last): File "/home/projects/cu_10010/programs/DiscoSNP++-v2.2.10-bin-Linux/scripts/VCF_creator.py", line 120, in <module> if int(listline1[1]) & 2048 :#checks if it's not a secondary alignment => means splitted aligned sequence IndexError: list index out of range there was a problem with the VCF creation
If I change the -P parameter to 10 when running discoSNP this error disappear, presumably because the variant causing the problem is then skipped. Changing -k does not change anything. I would like to keep the parameters constant as I keep getting new samples and would prefer to have everything done with the same settings.
Anyone help would be appreciated.
Best, Ida
