Fasta sequence from Bam file

Question

[rse]

Hi,

Is there any way to retrieve the fasta sequence from the aligned bam file?

Thanks

Regards

[rse]

Thanks for your replies. I used the tools to convert my bam file to fastq format. Thereafter, i used seqtk to convert fastq to fasta format. But i am getting fasta sequence per read. If i want one sequence, how to do that?

[lieven.sterck]

of course you are. What are you expecting otherwise? one long concatenated sequence?

[rse]

Yes, i want to get one concatenated sequence.

[rse]

Do i need my variant calls for that? Thanks in advance

[GenoMax]

Yes you do. Here is a guide to do that.

BTW: You should have specified this in the original question since the answers you received are not what you are looking for.

[rse]

Yes, i agree. Should have specified. However, the generation of the consensus sequence works for SNVs and Deletions only. It fails for Insertions and Duplications. Moreover, the consensus sequence is highly dependent on the variant caller used.

[finswimmer]

Moreover, the consensus sequence is highly dependent on the variant caller used.

Yes, of course. So the question is why you are interested in a consensus sequence?

fin swimmer

[rse]

I am working on resolving insertions/ duplications/ translocations. I need to confirm the breakpoints by doing PCR and hence need the raw sequence to design the same. Is there a way that we can get the raw consensus FASTA that will act as a template for my PCR primer designing?

Answer 1

[finswimmer]

Similar question?

Works if you realy want to convert reads into fasta. And the print command maybe have to get adapted to what you want as the identifier. Or are you looking for a way to get a consensus sequence from the bam file? Than go ahead reading the linked thread.

fin swimmer

Answer 2

[lakhujanivijay]

A lot of different tools are available for the same. Read the docs carefully before you proceed to get the desired output

• bamtofastq

• bam2FastQ

• samtools fastq

• samtools bam2fq