manually paring down SAM files

[efoss]

I have created SAM files using BWA. BWA provides some optional fields like "Number of best hits". If I want to filter my data on the basis of some of these values, is there any problem in simply going through the file and deleting lines that don't pass whatever filter I choose? I would imagine that this would be fine, since it would be the same as if the read had never existed in the first place. But I can also imagine that there is some sort of line-numbering system in the SAM file and that when I start deleting various lines, that gets out of whack.

Eric

[nilshomer]

No line number in the SAM file. I would, however, mark them as unmapped so that if anyone in the future wants them, they are there.

[efoss]

No line number in the SAM file. I would, however, mark them as unmapped so that if anyone in the future wants them, they are there.

Thanks - I'm glad I can do this.

How do I mark the lines as unmapped rather than simply deleting them?

Eric

[nilshomer]

Set the flag field correctly. Verify the flag field with http://picard.sourceforge.net/explain-flags.html. The SAM format can help you explain the various bits (literally).

[efoss]

Set the flag field correctly. Verify the flag field with http://picard.sourceforge.net/explain-flags.html. The SAM format can help you explain the various bits (literally).

Thanks very much. I appreciate your help.

Eric