I'm trying to annotate my bacteria variants with SnpEff,
java -jar snpEff.jar -v Mycoplasma_hyopneumoniae_168_l /mnt/f/mycopn/variantcalling.vcf > /mnt/f/mycopn/res.ann.vcf
All my Reference and snpEff database are
Mycoplasma_hyopneumoniae_168_l, but I got into trouble.
The annotated vcf file contains empty ID column with
I read about the error, but could not get any hint how to fix it as I'm newbie.
Would you please help me? Best Regards...
what is the output of
how does it compare to the chromosomes of
the command you wrote returns:
and about second part, sorry Did you ask about aligner? I used hisat2.
how did you build/get the snpeff database for Mycoplasma_hyopneumoniae_168_l ?
for example in https://www.ncbi.nlm.nih.gov/nuccore/NC_017509.1 the genome could be named NC_017509.1 in snpeff , and not NC_021283.1
Oh sure, the snpEff downloaded the database itself,