realSFS statistics

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realSFS specifications

Information


Unique identifier OMICS_00071
Name realSFS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Source code URL http://128.32.118.212/thorfinn/realSFS/realSFS.tar.gz
Maintained Yes

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Maintainer


  • person_outline Thorfinn Sand Korneliussen <>

realSFS in pipeline

2018
PMCID: 5843647
PMID: 29520061
DOI: 10.1038/s41467-018-03384-9

[…] rna-seq reads (aligned using bowtie2 v. 2.2.3 to our evigene-enriched reference transcriptome), restricting analyses to the coding sequence of each transcript. first, we used the angsd dosaf and realsfs commands to calculate genotype likelihoods and the folded site frequency spectrum from the bam files. second, we used this site frequency spectrum as prior to calculate diversity measures […]


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realSFS in publications

 (20)
PMCID: 5843647
PMID: 29520061
DOI: 10.1038/s41467-018-03384-9

[…] rna-seq reads (aligned using bowtie2 v. 2.2.3 to our evigene-enriched reference transcriptome), restricting analyses to the coding sequence of each transcript. first, we used the angsd dosaf and realsfs commands to calculate genotype likelihoods and the folded site frequency spectrum from the bam files. second, we used this site frequency spectrum as prior to calculate diversity measures […]

PMCID: 5844301
PMID: 29301862
DOI: 10.1534/g3.117.300334

[…] of the number individuals in the subpopulation, while –setmaxdepth was set as five times the number individuals in the subpopulation. overall site frequency spectrum was then calculated with the realsfs program from the angsd package. using each subpopulation’s site frequency spectrum as prior, we then calculated θ for each subpopulation using angsd with the command:, angsd –b $bamlist –ref […]

PMCID: 5726641
PMID: 29232403
DOI: 10.1371/journal.pone.0189417

[…] a site frequency spectrum (sfs) for each population (dosaf; []) using paired-end bam files. two-dimensional sfs and global fst (weighted) between each population pair were then estimated using realsfs []., to calculate watterson’s theta [] and tajima’s theta [], sfs estimated as described above were used as priors (pest) with paired-end bam files to calculate each statistic for each site […]

PMCID: 5589899
PMID: 28883457
DOI: 10.1038/s41598-017-10666-7

[…] irgsp 1.0 (http://rapdb.dna.affrc.go.jp/) using soapaligner program. consensus sequences for each individual were generated by soapsnp. input file was prepared by samtools for snp calling with realsfs. population snp calling was performed with realsfs, based on the bayesian estimation of site frequency at each site. the likelihoods of genotypes for each individual were integrated and sites […]

PMCID: 5559211
PMID: 28835916
DOI: 10.1126/sciadv.1603198

[…] (dosaf) () using paired-end bam files for steelhead and single-end bam files for chinook. two-dimensional sfs and global fst (weighted) between each population pair were then estimated using realsfs ()., to calculate watterson’s θ (), tajima’s θ (), and tajima’s d (), we used sfs that were estimated as described above as priors (pest) with paired-end bam files to calculate each statistic […]


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