Question: questions about read groups
gravatar for BC357
3.8 years ago by
United States
BC35770 wrote:

As my prior question didn't seem to get a response, which was wrapped in my OP as a comment, I am re-posting it as a new question, hoping to get some feedback.

It seems that GATK tools require all files/input to be "read groups verified". However, I just realized the "commonly used setting" of BWA under Galaxy, for example, does NOT specify read groups in the output. My questions are

(a) Is there a reason why a critical piece of info like this is NOT selected as "commonly used" by default? (my understanding is that many non-GATK tools do not require the info of read groups, but to me this is hardly a good reason NOT to include it, especially when BAM is a file of a few MB to GB, adding read groups by default seems VERY innocuous)

(b) are all read groups (ID, CN, DS, DT, FO, KS, LB, PG, PI, PL, PU, SM) readily available in the original fastq? Is there a tool that could extract the info in the fastq and add them? If the info is not available in fastq, where could we find them (when all we have are just fastq files) ?

Any help? Thank you.

read groups • 1.0k views
ADD COMMENTlink modified 3.8 years ago by Jennifer Hillman Jackson25k • written 3.8 years ago by BC35770
gravatar for Jennifer Hillman Jackson
3.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The updated version of BWA will include the option to include read groups at the time of execution. Please see our test server for a preview:

Sorry that your follow-up question was overlooked, posting a new question for a new topic is generally the best strategy. Jen, Galaxy team

ADD COMMENTlink written 3.8 years ago by Jennifer Hillman Jackson25k

I should comment that all not fastq files are created alike. You can enter read groups as you like into the form. The values do not necessarily need to be strictly accurate. Auto-extraction is a good idea, but I am not sure how practical this is. How about we see how many votes this post gets .. if many, I'll open a Trello card for a tool request. Best, Jen, Galaxy team

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Jennifer Hillman Jackson25k
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