Filter alignments by read groups/sample

[June Deng]

Hi,

I have a BAM file containing multiple samples/read groups (paired-end sequenced) aligned to the same reference genome. I wish to only see one sample or read group at a time,

using IGV 2.3.90. there is no 'lflter alignments by read groups™ in the preference window. How else should I do it? Do i need a different version.

Thank you in advance

Best

June Deng

[James Robinson]

I'm sorry, I don't think we have that option.   Did you find it in earlier versions?

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[kevfe...@yahoo.com]

yes, I was looking for that too. It is referenced in the help section

On Wednesday, January 18, 2017 at 9:30:32 PM UTC-6, James Robinson wrote:

I'm sorry, I don't think we have that option.   Did you find it in earlier versions?

On Wed, Jan 18, 2017 at 6:28 PM, June Deng <june.s...@gmail.com> wrote:

Hi,

I have a BAM file containing multiple samples/read groups (paired-end sequenced) aligned to the same reference genome. I wish to only see one sample or read group at a time,

using IGV 2.3.90. there is no 'lflter alignments by read groups™ in the preference window. How else should I do it? Do i need a different version.

Thank you in advance

Best

June Deng

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[James Robinson]

Yes, you are correct.  The fields for setting this were inadvertently dropped from the Preferences dialog.   I will restore it for the next release, which will be sometime in the next 2 weeks.   In the meantime you can use the option by manually editing the "prefs.properties" file in the "igv" folder in the user home directory.  First make sure IGV is shut down.   Then open the file with a plain text editor and add the following lines

SAM.FILTER_ALIGNMENTS=true
SAM.FILTER_URL=/blah/blah/myFilterFile.txt

The "SAM.FILTER_URL" value needs to be either a full path to a file, or a URL.   The file contains read group names, 1 per line.

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[kevfe...@yahoo.com]

Thanks James. This will be good, but pointing to a file is not very interactive. Would it be possible to enter the read group names to include right there in the dialog box? 

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[James Robinson]

Yes, but it will require some development and I can't get to it immediately.    How interactive do you want it?  Preferences are meant to be long term, this capability was added to filter out known "bad" read groups permanently.   

To increase the odds this doesn't get forgotten I suggest opening an issue in our github repository:  https://github.com/igvteam/igv/issues.   We can continue the discussion there.

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