Post date: Nov 20, 2018 12:13:35 AM
## extract the appropriate SVs
perl findLumpySvs.pl lumpyids_sv_deletions.txt subset_luympy/del_genotyped.vcf
perl findLumpySvs.pl lumpyids_sv_dups.txt subset_luympy/dup_genotyped.vcf
perl findLumpySvs.pl lumpyids_sv_inversions.txt subset_luympy/inv_genotyped.vcf
grep -c ^Sc mod_*
mod_del_genotyped.vcf:194
mod_dup_genotyped.vcf:223
mod_inv_genotyped.vcf:25
Note that we are in good shape for the deletions and duplications, but we aren't matching most of the inversion. We do about twice as good, but still far from great if I only require the start or stop to match (but not both).
working in /uufs/chpc.utah.edu/common/home/u6000989/projects/timema_SV/SVs/popgen_lumpy_svs
perl vcf2gl.pl mod_del_genotyped.vcf
Number of loci: 194; number of individuals 20
perl vcf2gl.pl mod_dup_genotyped.vcf
Number of loci: 223; number of individuals 20
## ML freqs
perl runEstpEM.pl *gl
## split populations for gl files
perl splitPops.pl timema_SVs_lumpy_del.gl
perl splitPops.pl timema_SVs_lumpy_dup.gl
## ML freqs by population
perl runEstpEM.pl timema_SVs_lumpy_d*_*.gl
### looking at het
perl gl2h.pl timema_SVs_lumpy_del.gl p_timema_SVs_lumpy_del.txt
perl gl2h.pl timema_SVs_lumpy_dup.gl p_timema_SVs_lumpy_dup.txt
perl gl2genest.pl timema_SVs_lumpy_del.gl p_timema_SVs_lumpy_del.txt
perl gl2genest.pl timema_SVs_lumpy_dup.gl p_timema_SVs_lumpy_dup.txt