How to convert vcf file to frequency file for sweepfinder2
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24 months ago
1771012116 • 0

Hi, I am analysing genome wide scan for selective sweeps using SF2, but some problems blocked me. I appreciate if you could help me with the file conversion from VCF to desired allele frequency file. I have converted VCF file to frequency file in vcftools, but the file format generated with vcftools is not the same as expected, below is the few lines.

CHROM   POS     N_ALLELES       N_CHR   {ALLELE:FREQ}
chr1H   43870   2       46      C:0.891304      T:0.108696
chr1H   43895   2       44      A:0.909091      T:0.0909091
chr1H   43937   2       48      A:0.895833      G:0.104167
chr1H   43944   2       48      G:0.708333      T:0.291667
chr1H   43948   2       48      T:0.854167      A:0.145833
chr1H   44011   2       46      A:0.891304      G:0.108696


And below is the desired allele frequency file.

position x n folded
460000 9 100 0
460010 100 100 0
460210 30 78 1
463000 0 94 0


The first column is the position on the chromosome, the second column is the allele count ( ), the third column is the sample size ( ), and the fourth column is an indicator as to whether the site has been polarized (i.e., whether it is known that the allele is derived or ancestral)

Thank you in advance.

software error • 567 views
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Hi, have you been able to figure this out? I am also dealing with a similar issue.Thanks!