Question: Missing fields in Picard 'Collect Alignment Summary Metrics' tool(s)?
0
gravatar for Guy Reeves
2.9 years ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

HI 

 

 

When I run the Picard  'Collect Alignment Summary Metrics'  on usegalaxy.org on either .sam or .bam files the fields in the output for 'SAMPLE ' ,        LIBRARY'     and     'READ_GROUP   '   are all blank. I can see that in the sam file header that this information is available in the following line and RG is specified for each read (also GATK unified genotyper does not throw an error which looks for this info).

 

 

@RG ID:014L002 PL:ILLUMINA PU:500 LB:not_used PI:250 SM:s330 PG:pair_27_3_15 CN:500

It could of course be that I have over looked something, but it would be great if these field were reported as I dump output files directly into a database and this information would be useful to record.

This is a history which illustrates this for a .bam file and a converted. sam version  https://usegalaxy.org/u/guy1/h/read-group-check

Thanks  Guy

I have noticed that  .txt output file from at least one other PICARD  tool  also fail to report the same fields 'Insertion size metrics'.

 

 

 

 

ADD COMMENTlink modified 2.9 years ago by Anton Nekrutenko1.7k • written 2.9 years ago by Guy Reeves1.0k
1
gravatar for Anton Nekrutenko
2.9 years ago by
Penn State
Anton Nekrutenko1.7k wrote:

Guy:

There is a parameter called "The level(s) at which to accumulate metrics". Set it to "Read Group" and you will get data on per RG basis.

a.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Anton Nekrutenko1.7k

Dear Anton 

Thanks a lot for the reply.  I had not seen the "The level(s) at which to accumulate metrics". option as I had the tool in a workflow and that option is not available in that interface. To be honest to be useful to me I need to use it in a work flow (but I will find a work around).  I did however run the the tool from the main window and selecting 'read group' and unselecting 'all reads' does as you say does give values in the 'SAMPLE ' ,        LIBRARY'     and     'READ_GROUP   '   fields.  but I think something might be amiss as the value given for the .sam file with the info  in the original message gives '500'  rather than the expected '014L002'.  '500' could be either CN: or PN:  but not RG, unless I have missed something. 

Thanks again Guy

 

 

ADD REPLYlink written 2.9 years ago by Guy Reeves1.0k

Guy:

For backward compatibility there are TWO versions of picard at usegalaxy.org (the old version will soon be hidden). The one you want to use is in "NGS: Picard" category (not "NGS: Picard (beta)").  Simply replace the old version of the tool with the new one in your workflow. Let me know if this helps.

a.

ADD REPLYlink written 2.9 years ago by Anton Nekrutenko1.7k

Hi Anton.  Thanks

I had not noticed that there are currently two versions of Picard.  I can see that the new version outputs a tabular file rather than an html as in the earlier version-  I was aware that I saw seeing diffrent views but now I know why.

   As I mentioned above I think there might be mistake as in the 'Read group' field of the table I get the 'Platform unit (PU)' information from the .bam file header not the Read Group info. 

Thanks  Guy

 

 

 

 

 

ADD REPLYlink written 2.9 years ago by Guy Reeves1.0k
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