amrfinder eliminate_amrs_by_size

[bdecato]

Currently we arbitrarily remove AMRs that are less than half the gap limit in size. We reference this as a "hack that has produced excellent results" in the manual, but our conversation about hmr today got me thinking about size cutoffs.

Is it possible to implement something like hmr's size distribution/quantile cutoff approach in amrfinder? Would it be more appropriate?

[mengzhou]

I just realized that Fang has suggested a merging step for AMRs. She called those regions generated by amrfinder "partial AMRs" because they are very fragmented. Here's the command she sent me for merging AMRs.

awk '{if ($2 > 1000) {$2 -= 1000} else {$2 = 0} print $1,$2,$3 + 1000,$4,$5,$6}' sample.pamr | sortbed -c /dev/stdin | awk '{print $1,$2+1000,$3-1000,$4,$5,$6}' | awk '$3-$2 >= 200 && $3-$2 < 50000{print} ' > merged.amr

This command basically merges all regions that are within 1kb to each other and then filters by size >= 200bp.

[andrewdavidsmith]

Should this issue be updated or close @bdecato

[bdecato]

This is definitely something that should be standardized and hasn't been taken care of yet. @sarahsma when you are around next, let's talk about how it could be done.