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
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
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