Entering edit mode
6.8 years ago
samuel.lipworth
▴
30
Hi I have a vcf file from which I am calling: vcf-consensus filtered.vcf.gz < NC000962.fasta > test.fasta
There are bases in the new test.fasta which are different from the reference but not called as SNPs in filtered.vcf.gz - how can this be!? The VCF file is correct but I don't understand why there are a whole load of made up snps in the consensus fasta?
give us an example.