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It is the number of derived alleles. If you have n diploid samples. then you have 2n+1. The first entry is the frequency of having zero derived alleles. Second entry is the frequency of having one derived alleles. The last entry, which will be 2n+1 is the frequency of having 2n derived alleles. The first and the last category, are the invariable category.
On 24 Apr 2024, at 02.10, Erikacj ***@***.***> wrote:
I am running -doSaf and realSFS to obtain the SFS to estimate Ne through time. For 14 samples I run:
~/angsd/angsd
-bam bam.txt
-nThreads 8
-anc ~/ref.fasta
-setMinDepthInd 5
-doSaf 1
-minmapQ 30
-minQ 20
-minInd 7
-doBcf 1
-domajorminor 1
-gl 2
-dopost 1
-domaf 2
-out ./angsd/SFS
~/angsd/misc/realSFS SFS.saf.idx -maxIter 100 -P 4 > SFS.sfs
The output from the above gives me 29 numbers for 14 samples:
2553445.800865 103809.213969 43688.859571 28674.860202 21990.861158 17054.914529 14721.903145 12352.277563 11707.233481 10945.865687 11070.809709 10355.972034 10011.312219 9803.119318 9387.831696 5617.122029 4253.325799 2615.508075 2468.261782 1593.288319 1148.791966 1317.130954 1039.779926 1126.637310 1217.816215 1393.024173 1699.225106 2439.155779 18558.097422
I thought this should give me 28 numbers, not 29. Can someone explain why I am getting this number?
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I am running -doSaf and realSFS to obtain the SFS to estimate Ne through time. For 14 samples I run:
~/angsd/angsd
-bam bam.txt
-nThreads 8
-anc ~/ref.fasta
-setMinDepthInd 5
-doSaf 1
-minmapQ 30
-minQ 20
-minInd 7
-doBcf 1
-domajorminor 1
-gl 2
-dopost 1
-domaf 2
-out ./angsd/SFS
~/angsd/misc/realSFS SFS.saf.idx -maxIter 100 -P 4 > SFS.sfs
The output from the above gives me 29 numbers for 14 samples:
2553445.800865 103809.213969 43688.859571 28674.860202 21990.861158 17054.914529 14721.903145 12352.277563 11707.233481 10945.865687 11070.809709 10355.972034 10011.312219 9803.119318 9387.831696 5617.122029 4253.325799 2615.508075 2468.261782 1593.288319 1148.791966 1317.130954 1039.779926 1126.637310 1217.816215 1393.024173 1699.225106 2439.155779 18558.097422
I thought this should give me 28 numbers, not 29. Can someone explain why I am getting this number?
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