IndexError

[khyati-sb]

Hi

I am trying to use your script VCF2fasta.py, and as per the requirements I have used indexed and compressed files for reference genome as well as vcf file. My vcf file is multi-sample file. Also, Gff file used here is from NCBI Refseq database. I also removed comments from gif file as described in Issue3 Yet, somehow I am getting the following error while running:

python /home/bcgrc/bin/vcf2fasta/vcf2fasta.py -f Ref_70-15.fa -g Ref_70-15.gff -e gene -v all_snps.vcf.gz

Reading GFF file [Ref_70-15.gff] ... Traceback (most recent call last):
File "/home/bcgrc/bin/vcf2fasta/vcf2fasta.py", line 470, in
main()
File "/home/bcgrc/bin/vcf2fasta/vcf2fasta.py", line 78, in main
gff = filterFeatureInGFF(ReadGFF(args.gff), args.feat)
File "/home/bcgrc/bin/vcf2fasta/vcf2fasta.py", line 405, in ReadGFF
geneNames = getGeneNames(file)
File "/home/bcgrc/bin/vcf2fasta/vcf2fasta.py", line 378, in getGeneNames
last = processGeneName(fields[8])
IndexError: list index out of range

Also, I am trying to convert vcf to Fasta for all the region, Not just restricted to gene or CDS.
Your help is much appreciated.

[skaul31]

I have been having this same issue and have not been able to solve it. Were you able to figure out what the problem was?

[vkulaganathan]

Check if there are mismatches among reference.fa, the gff file & your input vcf.gz files in terms of Chromosome position entries.
In all the files, there should be consistency in the nomenclature of CHR position entries and gene id nomenclature.