Get Reference file from BAM

Question

[win]

Is is possible to determine the reference file from a BAM file? I want to programmatically determine the reference file that was used during alignment and use it for variant detection.

[Dan D]

Are you wanting to compute the content of the reference (i.e. the FASTA sequence) or just the name of the reference file?

[win]

I just need the name of the reference file so I can use it for pulling up variants.

Answer 1

[donfreed]

Besides the @SQ header lines, the bam file header may have information on the reference used in the @PG lines. If this header line is present, you can parse it to determine the reference which was used for alignment. An example line from a BWA mem aligned bam file is below.

@PG    ID:bwa  PN:bwa  VN:0.7.9a-r788-dirty    CL:bwa mem -t 6 -R @RG\tID:foo\tSM:bar /mnt/data/reference/hs37d5.fa ../ERR194147_1.fastq.gz ../ERR194147_2.fastq.gz

Which shows that this bam file was aligned to hs37d5.fa

[win]

Thanks. Is there a way to extract this info programmatically?