problem vcf format with

[mrouard]

Hello,

For some reasons, VCF filtered by GATK v4 may produce a different tag by adding the assembly information next to the contig size.
##contig=<ID=mito8,length=456355,assembly=Musa_genomes_V2.fasta>

Then this error occurs as the scripts expects only a integer

Traceback (most recent call last): File "vcf2allPropAndCov.py", line 375, in <module> if __name__ == "__main__": __main__() File "vcf2allPropAndCov.py", line 338, in __main__ chr_info = get_chr_size(data) File "vcf2allPropAndCov.py", line 220, in get_chr_size return [split_on_eq[2].split(',')[0], int(split_on_eq[3])] ValueError: invalid literal for int() with base 10: '456355,assembly'

[guiguimartin]

We modified the code so that there should be no problems now. Could you try and verify that it works now?
And sorry for the delay in response...