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Old 01-15-2016, 07:16 AM   #1
thh32
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Default How to get SNP abundance from a metagenomic VCF?

So I have a VCF:
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
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.
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