Hi thank you for your attention This is an example of the data format . I should change only first column (names to rs format)

Name Chr Position WDS2.GType WDS2.Log R Ratio WDS2.B Allele Freq

250506CS3900140500001_312.1 23 26298017 AA 0.1586 0.0009

250506CS3900218700001_1294.1 2 148802744 AB 0.1641 0.4478

250506CS3900283200001_442.1 1 188498238 AB 0.0914 0.4470

CL635241_413.1 3 182202867 BB 0.0718 1.0000

CL635750_128.1 3 223741135 AB 0.0265 0.4830

CL635944_160.1 6 114778683 BB -0.3251 0.9972

Contig35697_5761.1 6 18835475 BB -0.1425 0.9970

CZ924211_329.1 2 106470676 AB -0.1050 0.49

OAR3_207847578_X.1 3 193150848 AB -0.0122 0.4828

OAR3_211362922_X.1 3 196313951 AA 0.1171 0.0039

oar3_OAR1_119450287 1 119450287 AA -0.1919 0.0176

oar3_OAR1_119458232 1 119458232 AA -0.1807 0.00

OAR6_114756902_X.1 6 104240372 BB 0.0654 1.0000

OARUn.515_157736.1 15 48287818 BB -0.0536 0.9887

OARUn.54_510669.1 16 70664506 AA -0.4320 0.0129

OARUn.992_104641.1 18 12223461 BB 0.1197 0.9962

OARUn.992_53657_X.1 18 12171867 AA 0.0340 0.0066

s00002.1 0 0 AB -0.0878 0.4830

s00007.1 20 32340549 BB 0.0397 0.9956

s00014.1 6 48965903 BB -0.0218 1.0000

Hi hosein_salehi6

It can be tricky dealing with non-reference species. I quickly wrote a script in python that uses the chromosome and position in the text you posted and queries a VCF file with ovine SNPs (sourced from dbSNP 150 apparently). I assumed your results are tab delimited. I accessed the vcf from ensembl:

http://useast.ensembl.org/info/data/ftp/index.html

The script is not quick because it goes through all 6 million variants in the VCF file, but it worked on the sample you provided. Also, some of the variants will not be in the vcf file (like the variant on chromosome 0 and position 0 in the text you posted). For these SNPs the result will print out with "not in vcf file".

Note that you'll want to make sure the genomes used for your snpchip and this VCF file are the same, otherwise your results will be incorrect.

To run the script, copy and paste the code below into a text editor and save it as "sheep_snps.py". Then execute python sheep_snps.py <query_file> <vcf_file> > <output_file>

#!/usr/bin/python

from __future__ import print_function
import sys

snp_dict = {}

with open(sys.argv[1], 'r') as ovine:
    for line in ovine:
        line = line.rstrip()
        if "\"" in line:
            continue
        else:
            query_chrom = line.split("\t")[1]
            query_pos = line.split("\t")[2]
            identifier = query_chrom + "_" + query_pos
            snp_dict[identifier] = line


vcf_dict = {}

with open(sys.argv[2], 'r') as vcf:
    for line in vcf:
        line = line.rstrip()
        if "#" in line:
            continue
        else:
            ref_chrom = line.split("\t")[0]
            ref_pos = line.split("\t")[1]
            ref_identifier = ref_chrom + "_" + ref_pos
            vcf_dict[ref_identifier] = line.split("\t")[2]

for k,v in snp_dict.iteritems():
    try:
        print(vcf_dict[k],v, sep = "\t")
    except:
        print("not_in_vcf_file",v, sep = "\t")

and the results look like:

rs407034953      Contig35697_5761.1            6   18835475   BB  -0.1425  0.9970
rs423741346      OARUn.992_104641.1            18  12223461   BB  0.1197   0.9962
rs55630697       250506CS3900283200001_442.1   1   188498238  AB  0.0914   0.4470
rs420791893      CL635750_128.1                3   223741135  AB  0.0265   0.4830
rs404585538      s00014.1                      6   48965903   BB  -0.0218  1.000
rs428970013      oar3_OAR1_119458232           1   119458232  AA  -0.1807  0.00
rs399786672      CL635944_160.1                6   114778683  BB  -0.3251  0.9972
rs413235350      OAR3_207847578_X.1            3   193150848  AB  -0.0122  0.4828
rs420600628      OAR6_114756902_X.1            6   104240372  BB  0.0654   1.0000
rs400403799      OARUn.515_157736.1            15  48287818   BB  -0.0536  0.9887
rs411856398      OARUn.54_510669.1             16  70664506   AA  -0.4320  0.0129
rs414154811      s00007.1                      20  32340549   BB  0.0397   0.9956
rs429408796      oar3_OAR1_119450287           1   119450287  AA  -0.1919  0.0176
rs413244887      CZ924211_329.1                2   106470676  AB  -0.1050  0.49
rs55630642       250506CS3900140500001_312.1   23  26298017   AA  0.1586   0.0009
rs55630663       250506CS3900218700001_1294.1  2   148802744  AB  0.1641   0.4478
rs409664674      CL635241_413.1                3   182202867  BB  0.0718   1.0000
rs402411363      OARUn.992_53657_X.1           18  12171867   AA  0.0340   0.0066
not_in_vcf_file  s00002.1                      0   0          AB  -0.0878  0.4830
rs401152114      OAR3_211362922_X.1            3   196313951  AA  0.1171   0.0039