Question: extracting Individuals containing the SNP from a vcf file
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gravatar for akang
2.7 years ago by
akang90
akang90 wrote:

I have an illumina SNP VCF file. Also i have a list of SNPs (rs number or the position ) that are associated with some diseases. I want to extract the individuals that contain the SNP. I am new to VCF file so ill appreciate any help! I can see there are some individuals having this mutation by typing

grep '751586' Input.vcf

I have a list like so

g.751586T>C
g.75787A>G

VCF file: Input.vcf

15  751586  rs12345 T   C   45777.47    PASS    AC=187;AF=0.688;AN=272;BaseQRankSum=3.218;DB;DP=2466;Dels=0.00;FS=1.917;HaplotypeScore=2.8099;InbreedingCoeff=-0.0808;MLEAC=187;MLEAF=0.688;MQ=41.01;MQ0=2;MQRankSum=5.767;QD=20.14;ReadPosRankSum=0.258;SOR=0.885  GT:AD:DP:GQ:PL  1/1:0,20:20:48:433,48,0 0/1:4,8:12:22:205,0,22  1/1:0,13:13:39:369,39,0 1/1:0,14:14:30:282,30,0 1/1:0,20:20:45:427,45,0 1/1:0,19:19:48:451,48,0 0/1:7,9:16:99:108,0,131 1/1:0,15:15:42:423,42,0 0/1:9,7:16:99:146,0,177 0/1:11,7:19:97:97,0,176 1/1:0,13:13:30:285,30,0 1/1:0,10:11:24:224,24,0 0/1:2,8:11:10:161,0,10  1/1:0,11:13:18:168,18,0 1/1:0,18:18:33:310,33,0 1/1:0,10:10:27:257,27,0 1/1:0,3:3:9:95,9,00/1:5,9:14:85:137,0,85    1/1:0,6:6:15:147,15,0   1/1:0,9:9:27:272,27,0   1/1:0,10:10:27:286,27,0 0/0:14,0:14:33:0,33,307 1/1:0,6:6:18:183,18,0   0/1:2,3:5:18:80,0,18    1/1:0,10:10:30:301,30,0 0/1:10,6:16:99:105,0,190    0/1:8,6:14:83:83,0,155  0/1:11,9:20:99:218,0,144    0/0:16,0:16:39:0,39,358 1/1:0,7:7:21:211,21,0   0/1:7,11:18:44:236,0,44 1/1:0,9:9:24:228,24,0   0/1:8,5:13:88:88,0,127  0/1:5,4:9:70:70,0,76    1/1:0,20:20:57:541,57,0 0/1:6,12:19:47:244,0,47 1/1:0,26:26:57:546,57,0 0/1:12,7:20:92:92,0,254 0/1:6,8:14:99:107,0,102 0/1:12,9:21:99:141,0,221    0/0:22,0:22:45:0,45,436 1/1:0,22:22:54:515,54,0 1/1:0,25:25:72:724,72,0 1/1:0,18:19:39:351,39,0 0/1:6,13:19:98:316,0,98 0/1:6,10:16:99:233,0,146    0/1:12,9:21:99:229,0,237    1/1:1,30:31:60:875,60,0
snp vcf • 873 views
ADD COMMENTlink written 2.7 years ago by akang90
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