Can I extract a complete sequence of gene from mapped reads bam file

Question

[singhankit973]

Can I extract gene sequences from mapped reads?

I have mapped Illumina paired WGS against a reference genome. By using locus ID of gene I extracted a bam file (gene.bam) of that gene from my mapped reads. Now what should I do next to extract complete sequence of gene from gene.bam file.

I have Locus ID, protein ID, Chromosomal location of gene in reference genome and reference genome annotation file, and the size of reads is 90 bp.

[Pierre Lindenbaum]

see FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker

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[singhankit973]

I'm sorry, I couldn't understand, i'm new to this, can you elaborate what you want to say?

[swbarnes2]

What have you tried so far?

[rfran010]

It sounds like you want to get the consensus sequence for a particular locus? Does this thread help you? Generating consensus sequence from bam file or maybe http://www.htslib.org/doc/samtools-consensus.html ?