Commit f234653c authored by peguerin's avatar peguerin
Browse files

stacks 2.2 step4 update

parent 5bbb4c97
......@@ -51,12 +51,13 @@ rule run_populations:
params:
r=config["populations"]["r"],
p=config["populations"]["p"],
f=config["populations"]["f"],
a=config["populations"]["a"],
fst_correction=config["populations"]["fst_correction"],
min_maf=config["populations"]["min_maf"],
p_value_cutoff=config["populations"]["p_value_cutoff"],
lnl_lim=config["populations"]["lnl_lim"]
lnl_lim=config["populations"]["lnl_lim"],
renz=config["populations"]["renz"]
log:
'10-logs/populations/{species}.log'
shell:
'''mkdir -p {output};
populations -t {threads} -P {input.gdir} -M {input.popm} -r {params.r} -p {params.p} -f {params.f} -a {params.a} --p_value_cutoff {params.p_value_cutoff} --lnl_lim {params.lnl_lim} --write_single_snp --vcf --vcf_haplotypes --structure -O {output} > {log}'''
populations -t {threads} -P {input.gdir} -M {input.popm} -r {params.r} --fst_correction {params.fst_correction} --min_maf {params.min_maf} --p_value_cutoff {params.p_value_cutoff} --lnl_lim {params.lnl_lim} --write_single_snp --vcf --vcf_haplotypes --merge_sites --renz {params.renz} --structure -O {output} > {log}'''
......@@ -21,9 +21,11 @@ gstacks:
populations:
cores : 32
r : 0.85
p : 1
f : p_value
a : 0.05
p : 4
fst_correction : p_value
min_maf : 0.05
p_value_cutoff : 0.10
lnl_lim : -10
renz : SbfI
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