ID field of discosnp++

Question

[rutujagtap08]

Hi, Can anyone please elloborate the meaning of ID field in the VCF file generated by VCF_creator after running discosnp++. For example "INDEL_lower_path_2890" I am having this in my CHROM field and 2890 in ID field.

Thanks, Rutuja

Answer 1

[pierre.peterlongo]

Hi -

If the VCF file was created with a reference genome, it may appear that some predicted variants are not mapped on the genome. If it was created without a reference genome, none of them are mapped.

When a variant is not mapped to a reference genome, the chrom field indicates the id of the prediction (here "INDEL_lower_path_2890") and the mapping position indicates the position of the variant (here an INDEL) on the sequence of the bubble of the variant. Actually, in this case, the CHROM field does not add any piece of information wrt the fasta file.

Hope this helps, Pierre