search

tseemann / snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment
GNU General Public License v2.0
461 stars 113 forks source link

different refs with different .consensus.fa? #112

Closed indexofire closed 6 years ago

indexofire commented 6 years ago

I am doing virus mapping to get genomes. I dont get why I changed the reference of virus genome, snippy returned different snps.consensus.fa with about >30 snps differ. Is that means the method is worng to get virus genome? or Should I remove duplicates first?

anyone can help? thanks alot!

tseemann commented 6 years ago

If you change the reference genome, then yes, you will get a different number of SNPs between your reads and the reference?

The consensus will always be relative to the reference genome, so if there was locii in your sample they will not magically appear in the consensus. You need to use de novo genome assembly instead.

indexofire commented 6 years ago

The method is fine in virus genome mapping assembly I think. I will check if it's the pollution of different samples(highly similar in genomes, so the related reads vary the results) or the sample is a metagenomic ngs(virus mixed infection).

Thanks you very much.