error in binary nexus

[PRASADLIFE]

To convert the vcf into binary nexus it throw the error:-

Traceback (most recent call last): File "vcf2phylip.py", line 384, in main() File "vcf2phylip.py", line 224, in main binsite_tmp = ''.join([(gen_bin[broken[i][0:3]]) for i in range(9, index_last_sample)]) KeyError: '1|1'

[edgardomortiz]

I will need more info, what was your command? how did you generate your vcf? could you send the first. 5000 lines of your vcf to replicate the error?

[PRASADLIFE]

This is my command to get the binary nexus format.

python vcf2phylip.py -i 9983.vcf --phylip-disable -n --nexus-binary

I successfully converted the vcf to nexus but to convert into binary nexus it through the error. I attached the sample file. first_5000.vcf.gz

[edgardomortiz]

Thanks for reporting the bug, please test and if it works I will mark it as solved.

[PRASADLIFE]

Yes, now it's running. Thank You very much for the quick response.

[edgardomortiz]

Cool, no problem.