Dataset formats

The input dataset is VCF format. The output dataset is pgSnp. (Dataset missing?)

What it does

This converts a VCF dataset to pgSnp with the frequency counts being chromosome counts. If there is more than one column of SNP data it will either accumulate all columns as a population or convert the column indicated to pgSnp.

Examples

• input:

  1       13327   rs144762171     G       C       100     PASS    VT=SNP;SNPSOURCE=LOWCOV     GT:DS:GL        0|0:0.000:-0.03,-1.11,-5.00     0|1:1.000:-1.97,-0.01,-2.51     0|0:0.050:-0.01,-1.69,-5.00     0|0:0.100:-0.48,-0.48,-0.48
  1       13980   rs151276478     T       C       100     PASS    VT=SNP;SNPSOURCE=LOWCOV     GT:DS:GL        0|0:0.100:-0.48,-0.48,-0.48     0|1:0.950:-0.48,-0.48,-0.48     0|0:0.050:-0.48,-0.48,-0.48     0|0:0.050:-0.48,-0.48,-0.48
  1       30923   rs140337953     G       T       100     PASS    VT=SNP;SNPSOURCE=LOWCOV     GT:DS:GL        1|1:1.950:-5.00,-0.61,-0.12     0|0:0.450:-0.10,-0.69,-2.81     0|0:0.450:-0.11,-0.64,-3.49     1|1:1.500:-0.48,-0.48,-0.48
  etc.
  

• output as a population:

  chr1    13326   13327   G/C     2       7,1     0,0
  chr1    13979   13980   T/C     2       7,1     0,0
  chr1    30922   30923   G/T     2       4,4     0,0
  etc.
  

• output for each column separately:

  chr1    13326   13327   G       1       2       0       G/C     2       1,1     0,0     G       1       2       0       G       1       2       0
  chr1    13979   13980   T       1       2       0       T/C     2       1,1     0,0     T       1       2       0       T       1       2       0
  chr1    30922   30923   T       1       2       0       G       1       2       0       G       1       2       0       T       1       2       0
  etc.