pipeline and script for human-chimp sv affecting cis regulatory elements manuscript.
I will document my script in the coming weeks, maybe I will rewrite my bash script with snakemake.
point to the supplemental code once published.
python3 refine_calledSV.py --sv SV --bam BAM > calledSV.bed
Options:
--sv SV Annotated structural variations. DASVC pipeline output file.
--bam BAM BAM alignment file between the two species. Can be found in the DASVC pipeline.
python3 OrthoINDEL.py [-i INPUT] [-d MIN] [-m MAX] [-b] [-s] [-n] [-p PERC]
Options:
-i INPUT, --input INPUT The input crossmap output file.
-d MIN, --distance MIN The distance used to define continous regions. fragments within a region are considered continous if the gap is smaller than the distance. Default is 50bp.
-m MAX, --max MAX The distance used as upper limit of tolerated INDELs. Fragments separated by INDELs larger than the max distance will not be merged. Default is 50,000bp.
-b --broad If the input peaks are broadpeaks (broad peaks do not have summit defined).
-s --stringent If false, return splitted regions after final combination process. Default is True.
-n --noindel If True, only return regions without any indel > distance.
-p PERC --perc PERC The threshold to remove non-primary fragments (fraction of total region length).