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#283 SAM header info for @PG tags

v0.9.0
closed
Val
bowtie (175)
5
2014-01-29
2013-04-22
Anonymous
No

Dear
I ran following command using bowtie2 version 2.1.0.

bowtie2 --mm --threads 12 -q --phred33 --very-sensitive -N 1 -L 15 -i L,0,0.1 --end-to-end -k 20 -x ref.fa in.fq -S out.sam

I noticed that in the PG flag of the sam headers, it no longer writes the command line parameters as it is done with bowtie1.

i.e. CL tag value pair is missing.

Is it a bug or am I not using the program correctly?

Any help is greatly appreciated.

kind regards

Hardip

Discussion

  • Val
    Val
    2013-07-17

    Hi Hardip,

    bowtie2 does not have this feature. However this seem to be useful for some users and we will consider adding this in the future.

    I will leave this case open for now until we reach a resolution.

    Val

     
  • Val
    Val
    2014-01-29

    • status: open --> closed
    • assigned_to: Val
    • Group: --> v0.9.0
     
  • Val
    Val
    2014-01-29

    fixed