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Reconstruct reference sequence from SAM file?

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!

sam
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updated by WouterDeCoster WouterDeCoster • written by eholleman • eholleman

1 answer

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
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written by WouterDeCoster WouterDeCoster

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

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written by Pierre Lindenbaum Pierre Lindenbaum

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

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written by eholleman • 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?

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written by eholleman • eholleman

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