So I have a VCF:
This is from a metagenomic analysis where I have 10 samples with phenotype A and 10 with phenotype B.
I want to directly compare the abundance of each SNP in phenotype A and B but I am unsure if there are tools around which can do this for me or if I need to write my own code.
Any help would be great as I am very unfamiliar with SNP analysis.
HTML Code:
NODE_2672_length_273_cov_23.978022 190 . G T 275 . DP=217;VDB=3.00218e-07;SGB=-0.477013;RPB=0.289765;MQB=6.34926e-08;MQSB=0.867801;BQB=0.982133;MQ0F=0;ICB=0.78125;HOB=0.111111;AC=8;AN=24;DP4=71,91,23,22;MQ=26 GT:PL:DP:DV:SP:DPR 0/0:0,5,138:10:3:7:7,3 0/0:0,4,167:8:2:0:6,2 ./.:0,0,0:0:0:0:0,0 0/0:0,30,232:10:0:0:10,0 ./.:0,0,0:0:0:0:0,0 ./.:0,0,0:0:0:0:0,0 ./.:0,0,0:0:0:0:0,0 0/1:69,0,41:10:6:0:4,6 0/1:88,0,91:14:9:0:5,9 ./.:0,0,0:0:0:0:0,0 0/1:27,0,184:18:6:2:12,6 1/1:40,6,0:2:2:0:0,2 0/0:0,24,129:8:0:0:8,0 ./.:0,0,0:0:0:0:0,0 0/1:18,3,0:5:4:0:1,4 1/1:106,24,0:8:8:0:0,8 0/0:0,12,114:19:3:11:16,3 ./.:0,0,0:0:0:0:0,0 ./.:0,0,0:0:0:0:0,0 0/0:0,240,255:95:2:0:93,2 NODE_2672_length_273_cov_23.978022 193 . T C 70 . DP=214;VDB=0.000590394;SGB=4.35052;RPB=0.656362;MQB=6.38638e-05;MQSB=0.888189;BQB=1;MQ0F=0;ICB=0.084;HOB=0.03125;AC=3;AN=24;DP4=85,97,8,14;MQ=26 GT:PL:DP:DV:SP:DPR 0/0:0,27,133:9:0:0:9,0 0/0:0,5,171:9:1:0:8,1 ./.:0,0,0:0:0:0:0,0 0/0:0,27,219:9:0:0:9,0 ./.:0,0,0:0:0:0:0,0 ./.:0,0,0:0:0:0:0,0 ./.:0,0,0:0:0:0:0,0 0/1:41,0,69:10:4:0:6,4 0/0:0,42,199:14:0:0:14,0 ./.:0,0,0:0:0:0:0,0 0/0:0,54,234:18:0:0:18,0 0/0:0,6,40:2:0:0:2,0 0/1:47,0,53:8:4:8:4,4 ./.:0,0,0:0:0:0:0,0 0/0:0,3,18:5:1:0:4,1 0/0:0,24,106:8:0:0:8,0 0/1:34,0,70:19:12:31:7,12 ./.:0,0,0:0:0:0:0,0 ./.:0,0,0:0:0:0:0,0 0/0:0,255,255:93:0:0:93,0
I want to directly compare the abundance of each SNP in phenotype A and B but I am unsure if there are tools around which can do this for me or if I need to write my own code.
Any help would be great as I am very unfamiliar with SNP analysis.