Open eriqande opened 2 years ago
This is where I am going to be writing short things that I update.
Here is an example path:
"results/bcf_{bcf_id}/filt_{bcfilt}/{sampsub}/thin_{thin_int}_{thin_start}/pcangsd/maf_{min_maf}
{bcf_id}
{bcfilt}
{sampsub}
{thin_int}_{thin_start}
thin_int
thin_start
{min_maf}
{npc}
This is where I am going to be writing short things that I update.
Wildcards in play and path structure
Here is an example path:
"results/bcf_{bcf_id}/filt_{bcfilt}/{sampsub}/thin_{thin_int}_{thin_start}/pcangsd/maf_{min_maf}{bcf_id}: identifier for the particular BCF file{bcfilt}: nickname for the set of bcftools filtering options{sampsub}: nickname for the sample subset{thin_int}_{thin_start}:thin_intis the thinning interval (i.e., take every thin_int-th variant) andthin_startis where you should start from.{min_maf}: in pcangsd and ANGSD applications that have MAF filtering, this denotes the value.{npc}: the number of principle components retained and put into the dotsample (for now). May get used elsewhere.