Generate consensus sequence from BAM alignment

[Adam Witney]

Hi,

I have a BAM file and I would like to generate a consensus sequence or a set of contigs (if there are gaps in the alignment). My google search seems to only come up with generating consensus reads... are there any tools that can produce contigs?

Thanks

adam

[francois.sabot]

Hi
One overcome for that is to generate a VCF file from BAM and then extrapolate your sequence based on your ref. We have performed that using a simple home-made script and VCF file with all site expressed (you juste need to extract the 5th column). Gaps will be points, you can cut your contig if more than 20 points appear, eg.

Some tools such as NovelSeq seem to be able to 'fill the gaps', ie to add the extra sequences from the sequenced target vs the ref sequence.

Hoping it will help

F.

[Adam Witney]

thanks for the advice, I'll give it a try

adam