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SouthGreenPlatform / VcfHunter

VcfExplorer regroups several programs which principal aims are to map DNA and RNAseq data onto reference genome sequence, perform variant calling, manipulate vcf files, perform chromosome painting of accessions based on the contribution of ancestral groups, select marker for genetic map analysis and perform pairwise chromosome linkage of ordered markers.
GNU General Public License v3.0
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problem vcf format with #2

Open mrouard opened 4 years ago

mrouard commented 4 years ago

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 commented 3 years ago

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...