HOR Structural Variant (StV) prediction using HOR-monomer annotation
Usage: ./stv.sh input.bed
Note: input.bed must be sorted (bedtools sort) and must contain the HOR monomers. You can generate it from sequence using HumAS-HMMER for example.
Config: insert path to dir with program into stv.sh
Output files:
• stv.bed - resulting file which can be put in the browser
• stv_raw.bed - same as stv.bed but doesn't contain stv numbering, colors, the first description line
• stv_stats.tsv - contains the number of each stv in each chr/contig
Method:
- Extract only "live HORs" from the input bed.
- Iterate through AS_liveHORs.bed merging monomers. StV is cut after the last monomer (the one with maximal number in a given array) or before the first monomer (or vice versa in the case of a "-" strand).
- Squeeze huge "6/4_5" dimer stretches in the human cen1/cen5/cen19.
- Count StV stats.
- Add numbering and colors.
Here is special version for T2T-CHM13 assembly which was used in the "Complete genomic and epigenetic maps of human centromeres" article.