bowtie priduced SAm file does not have RG tags in alignment

[neha]

Hello Everyone,

I have used bowtie for mapping my reads to human genome. Bowtie directly outputs the SAM file using -S option but then I realized that SAM file produced does not have the RG tags which is required by various other software Like GATK for variant analysis.

I figured out the way to add the RG tags in header section, but still it does not provide these tags in alignment section.

Does anyone has faced this problem before and any advice would be appreciated.

Thanks and Regards,
Neha

[dariober]

Hello Everyone,

I have used bowtie for mapping my reads to human genome. Bowtie directly outputs the SAM file using -S option but then I realized that SAM file produced does not have the RG tags which is required by various other software Like GATK for variant analysis.

Hello- Have a look at Picard AddOrReplaceReadGroups it should do what you need.

Dario

[kmcarr]

I have used bowtie for mapping my reads to human genome. Bowtie directly outputs the SAM file using -S option but then I realized that SAM file produced does not have the RG tags which is required by various other software Like GATK for variant analysis.

Both Bowtie and Bowtie2 can add read group information to the SAM output, but do not by default. You have to provide the information through command line options when you run Bowtie(2). The two versions of Bowtie have different options for adding read group information.

Bowtie uses the option --sam-RG option to add TAG:VALUE pairs to build the full read group definition. --sam-RG is used multiple times, once for each TAG:VALUE to be added to the read group definition; at a minimum the TAGs ID and SM (sample) must be included in the definition.

Example:
--sam-RG ID:HWI-SN957Lane7 --sam-RG SM:ZEN456A1 --sam-RG LB:ZEN456A1LI5 --sam-RG PI:400 --sam-RG PL:ILLUMINA

Bowtie2 is very similar except that it has separate options for specifying the read group ID (--rg-id) used only once on the command line and other read group TAG:VALUE pairs which may be used multiple times. If you use the --rg option you must also supply the --rg-id option.

Example:
--rg-id HWI-SN957Lane7 --rg SM:ZEN456A1 --rg LB:ZEN456A1LI5 --rg PI:400 --rg PL:ILLUMINA

Of course this won't help you for the SAM file you already have; in this case dariober's suggestion about Picard's AddOrReplaceReadGroups is the way to go.

[neha]

Thanks kmcarr and Dario. I will try Picard utility and hope it will solve my problem.

Thanks,
Neha