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ANGSD / angsd

Program for analysing NGS data.
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2d folded sfs how to? #599

Open darijajosic opened 11 months ago

darijajosic commented 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

TrishikaS commented 10 months ago

Hey @darijajosic, that seems ok to me. Did it work?