How to get SNP abundance from a metagenomic VCF?

thh32

Member

Join Date: Feb 2014
Posts: 60

How to get SNP abundance from a metagenomic VCF?

01-15-2016, 08:16 AM

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.

Tags: metagenome, snp, snp analysis, vcf, vcf analysis tools

Previous template Next

Current Approaches to Protein Sequencing

by seqadmin

Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
- Channel: Articles
04-04-2024, 04:25 PM
Strategies for Sequencing Challenging Samples

by seqadmin

Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
- Channel: Articles
03-22-2024, 06:39 AM

Topics	Statistics	Last Post
Cancer Metastasis: A Deep Dive into Cellular Plasticity by seqadmin Started by seqadmin, 04-11-2024, 12:08 PM	0 responses 18 views 0 likes	Last Post by seqadmin 04-11-2024, 12:08 PM
Proteogenomic Profiles Offer New Clues in Prostate Cancer by seqadmin Started by seqadmin, 04-10-2024, 10:19 PM	0 responses 22 views 0 likes	Last Post by seqadmin 04-10-2024, 10:19 PM
Novel Diagnostic Assay Enhances Ovarian Cancer Detection by seqadmin Started by seqadmin, 04-10-2024, 09:21 AM	0 responses 16 views 0 likes	Last Post by seqadmin 04-10-2024, 09:21 AM
Evolutionary Dynamics of Centromeres: A Comparative Genomic Analysis by seqadmin Started by seqadmin, 04-04-2024, 09:00 AM	0 responses 47 views 0 likes	Last Post by seqadmin 04-04-2024, 09:00 AM

Seqanswers Leaderboard Ad

Announcement

How to get SNP abundance from a metagenomic VCF?

Latest Articles

ad_right_rmr

News