Deletions in a consensus sequence.

Question

[kspata]

Hi All,

I performed alignment of merged forward and reverse read for a plasmid sequence. From this I wanted to observe deletion in a specific location. I extracted all reads from the BAM file in the region 10000-10040. I found that around 600 reads mapped to this position and out of them 200 had deletions. Now I want to generate consensus sequence for the entire plasmid but it should have all these deletions present in the consensus.

How can i generate a consensus which shows deletions as variants?

Your help will be appreciated. Thanks in advance!!!

[finswimmer]

Hello,

first you have to do a variant calling. Afterwards use bcftools consensus to create consensus sequence.

fin swimmer

[kspata]

Hi Fin,

I have performed variant calling but these variants are not called with samtools as they are very large deletions (>35bp) present at low frequency (<10%). Even if they are at low frequency I wish to include them in the consensus sequence. So that when I perform BLAST of reference vs consensus it will show these deletions. Is there any tool which can be used to analyze low frequency large Deletions and generate consensus representing the deletions?

Thanks for replying!!