KeyError: PI

[vappiah]

Hi I was trying to convert my vcf to haplotype . I used python3.6 to run vcf-simplify and I got the error message below

Traceback (most recent call last):
File "/home/user/apps/VCF-Simplify/VcfSimplify.py", line 58, in
main()
File "/home/user/apps/VCF-Simplify/VcfSimplify.py", line 53, in main
vcf_solver(task, args)
File "/home/user/apps/VCF-Simplify/assign_task/perform_operation.py", line 95, in vcf_solver
fnc_vcf_to_haplotype(infile, outfile, header_name, pi_tag, pg_tag, include_unphased, gtbase)
File "/home/user/apps/VCF-Simplify/metadata_parser/utils.py", line 26, in wrapper
result = func(*args, **kwargs)
File "/home/user/apps/VCF-Simplify/records_parser/simplifyvcf/to_haplotype.py", line 101, in fnc_vcf_to_haplotype
pi_values = [mapped_record[sample][pi_tag] for sample in sample_ids]
File "/home/user/apps/VCF-Simplify/records_parser/simplifyvcf/to_haplotype.py", line 101, in
pi_values = [mapped_record[sample][pi_tag] for sample in sample_ids]
KeyError: 'PI'

[everestial]

It's because your VCF does not have the "PI" tag in FORMAT field. You may indicate any other equivalent tag or "CHROM" if you want the haplotype representation to be chromosome wide.