allelotype BAM readgroups

[wendy wong]

Hi,

I just tried running LobSTR allelotype and it worked really well!  

We have BAM files of trios (parents and probing) from Illumina Services, so the BAM readgroup SM tag is the sample ID, but the readgroup LB tag is perhaps lane ID (usually 0, 1 and 2). I would like to do multisample calling for each trio but since the readgroup IDs are the same it treats them to be one sample? As I only get calls for the first BAM files I inputted. I cannot rewrite the BAM files and do not want to recreate them with the corrected readgroup LB tag. I was wondering if there's anything I could do about this? 

Thanks,

Wendy

[Melissa Gymrek]

Hi Wendy,

Great to hear you got allelotype running smoothly. LB should not be a problem. But unfortunately, if the read group ID is the same for multiple samples, there is no currently no way to tell them apart.  For a given read, the read group info usually just contains the read group ID, and other information like sample are obtained from the header. If read group IDs are duplicated, it won't know which sample it's from. Right now the options are to run allelotype separately on those or to use a tool like Picard's AddOrReplaceReadGroups to change the ID. I will make an issue for this and hopefully we can do something about it for the next release.

Best,

~Melissa

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[wendy wong]

Hi Melissa,

Thanks for your detailed explanation. I understand it now. It would really be great if it could be addressed in the next release!

I am keen to use lobSTR on our trios and have another question - will start a new thread. 

Best,

Wendy

[takic...@gmail.com]

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