This tool really impressed me, as I have benn having a hard time working with samtools and picard. They do work, but not straightforward.
As for realign I would thought the unmaped read is also needed. so I use "-L 0:0-0" to get them and it seem that stratege just work, but seem to have potential including unwant reads with only one of paired reads unmapped.
I think it could be a feature to add option for including reads with both end unmaped.
And also, since the bam file is sorted, would read through the whole bam still nesseary for target region? Would there be a strategy for small target selection?
This tool really impressed me, as I have benn having a hard time working with samtools and picard. They do work, but not straightforward.
As for realign I would thought the unmaped read is also needed. so I use "-L 0:0-0" to get them and it seem that stratege just work, but seem to have potential including unwant reads with only one of paired reads unmapped. I think it could be a feature to add option for including reads with both end unmaped.
And also, since the bam file is sorted, would read through the whole bam still nesseary for target region? Would there be a strategy for small target selection?