Cannot get specific sample IDs in SAM alignment using Bowtie2

[erms]

Hi,
I am trying to map WGS sample data to a set of reference genomes (bacterial) using Bowtie2. I have read the manual and have included the --rg-id option but if I am understanding it correctly, this requires that you specify a specific sample ID. I have hundreds of samples and cannot imagine that this is the only way to include that information in the alignment file.

This is what I am doing:
bowtie2 -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 -q --rg-id <text?> -x ref.Index -1 reads_1.fastq -2 reads_2.fastq -S reads_mapped.sam

Whatever is written after --rg-id is included verbatim after @RG and RG:Z: Is there some way to reference the correct position in the fastq file in the command above to include the specific sample ids?

Thank you!

[dpryan]

Read group IDs are independent of positions in a file, so no, that's not possible and would rather defeat the purpose of read groups. The purpose of read groups is to be able to keep groups of alignments together for downstream processing (in practice, this just means variant calling) depending on the original sample they came from, library batch, machine used to sequence them, etc.. None of those things would vary within an alignment file.

[erms]

Thank you for your answer. I apologize that I am slow, and perhaps I am asking the wrong question. I would like to be able to identify the sample identities within the read groups because I am hoping to be able to link the identity/location of specific variants with other sample qualities.

[dpryan]

You have the nesting reversed. Read groups are nested in samples, not samples in read groups (though a read group can be a sample).

[dpryan]

Or rather, read group IDs are nested within sample IDs.