Question: How Can I Make Sweeps Input File?
gravatar for mary
6.9 years ago by
Bologna university
mary210 wrote:

dear all

I am trying to find some way for make a input file of sweep 1.1, for detect selection signature on bovine genome by bovine 50K bead chip . Sweep requires two files as input, a genotype data file and a snp info file. as below:

genotype data file 1331-1331FF12 T 1 3 3 2 1331-1331FF12 U 1 1 1 2 1331-1331FM13 T 1 3 3 2 1331-1331FM13 U 1 3 3 4 1331-1331MF14 T 1 1 3 4 1331-1331MF14 U 1 1 1 2 1331-1331MM15 T 1 1 3 4 - Column 1: the individual identifier. - Column 2: the chromosome identifier. For automates we should have two chromosomes per individual. We label the two chromosomes T for transmitted and U for un-transmitted, (but it can be anything eg. A and B.) - Columns 3 – N: each column gives the allele for one SNP in the order of its position on the chromosome. The alleles are represented as A=1, C=2, G=3, T=4.

The first row therefore represents one chromosome for individual 1331-1331FF12 with the haplotype AGAAT. The second row represents the other chromosome for individual 1331-1331FF12 with the haplotype AAGGC.

SNP info file snpid chr HG16 rs267265 3 45548733 rs267262 3 45567119 rs267241 3 45578901 rs2005227 3 45598847 rs267230 3 45619948 rs2012755 3 45633347

  • Column 1: The SNP identifier. This can be an rs number or any other name you choose to give.
  • Column 2: The chromosome.
  • Column 3: The SNP position based on the build identified. HG16 and HG17 are currently recognized.

I think, making this two file should be possible by PHASE as you can see in sweep 1.1 Documentation. dose any one know how can I make it thanks for any help

ADD COMMENTlink modified 6.7 years ago by Biostar ♦♦ 20 • written 6.9 years ago by mary210
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