Question: How Can I Make Sweeps Input File?
1
gravatar for mary
5.6 years ago by
mary200
Bologna university
mary200 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

• 1.4k views
ADD COMMENTlink modified 5.4 years ago by Biostar ♦♦ 20 • written 5.6 years ago by mary200
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1523 users visited in the last hour