Reconstruct reference sequence from SAM file?

Question

[eholleman]

I am aligning a consensus sequence to a reference genome using Bowtie2 and I am interested in the nucleotide sequence of the reference where the consensus sequence aligned. Is it possible to infer the reference sequence using only information in the SAM file such as the CIGAR and MD strings? Thanks!

Answer 1

[WouterDeCoster]

Based on your alignment you can get the chromosome, start and end of where your consensus sequence aligns. You can use these coordinates with samtools faidx

samtools faidx yourgenome.fa chr1:123456-789101

[Pierre Lindenbaum]

I think OP only want the sequence from the BAM, not the REF.

[eholleman]

I am looking for the sequence in the reference that the query aligned to

[eholleman]

Thank you, this is what I am looking for. Would this be faster than building an indexed BLAST database and then using blastdbcmd to accomplish the same task?

[WouterDeCoster]

Yes I would assume so