Open darijajosic opened 11 months ago
Hi, I am probably doing this wrong... I am trying to produce a 2d folded sfs to use with fastsimcoal. My commands are as follows for each of my 2 populations:
angsd \ -nThreads 12 \ -bam bamlist_pop1 \ -anc m19_AffsNnoesSC.p1.fa \ -doSaf 1 \ -GL 2 \ -out pop1_sfs \ -minMapQ 30 \ -minQ 20
Next I fold it and create a 2d sfs:
realSFS -fold 1 pop1_sfs_red.saf.idx pop2_sfs_red.saf.idx -P 30 > pop1_pop2_fold_red.sfs
Is this the correct way?
Thank you so much for your help. Best, Darija
Hey @darijajosic, that seems ok to me. Did it work?
Hi, I am probably doing this wrong... I am trying to produce a 2d folded sfs to use with fastsimcoal. My commands are as follows for each of my 2 populations:
Next I fold it and create a 2d sfs:
realSFS -fold 1 pop1_sfs_red.saf.idx pop2_sfs_red.saf.idx -P 30 > pop1_pop2_fold_red.sfs
Is this the correct way?
Thank you so much for your help. Best, Darija