VCF Indel encoding question

darren.obbard

Junior Member

Join Date: Jan 2012
Posts: 5

VCF Indel encoding question

05-23-2013, 09:34 AM

Hi,

I'm having problems understanding a GATK output VCF. I have read the VCF standard, but I'm obviously missing something.

I /think/ I understand how SNPs and short indels are represented, but clearly I do not. Below is an excerpt that illustrates sites which I do not understand. I suspect it may be something to do with GATK quality filters that I'm not understanding...

The excerpt below was generated using

GATK -l INFO -I my.bam -R my.fa -T UnifiedGenotyper -S LENIENT -nt 8 --heterozygosity 0.1 -o test.vcf --genotype_likelihoods_model BOTH --min_base_quality_score 10 --output_mode EMIT_ALL_SITES -ploidy 2

Thanks!

Darren

-------------------------------------------------------

Code:

CH1	225	.	T	G	12.71	LowQual	AC=1;AF=0.500;AN=2;BaseQRankSum=1.978;DP=59;Dels=0.03;FS=0.000;HaplotypeScore=10.2840;MLEAC=1;MLEAF=0.500;MQ=70.25;MQ0=8;MQRankSum=-5.349;QD=0.22;ReadPosRankSum=-3.188	GT:AD:DP:GQ:PL	0/1:41,16:55:20:20,0,1435
CH1	226	.	T	.	121.53	.	AN=2;DP=59;MQ=70.25;MQ0=8	GT:DP	0/0:43
CH1	227	.	A	.	121.53	.	AN=2;DP=59;MQ=70.25;MQ0=8	GT:DP	0/0:43
CH1	228	.	T	.	121.53	.	AN=2;DP=59;MQ=70.25;MQ0=8	GT:DP	0/0:43
CH1	229	.	A	.	115.53	.	AN=2;DP=57;MQ=69.66;MQ0=8	GT:DP	0/0:38
CH1	230	.	C	.	115.53	.	AN=2;DP=57;MQ=69.66;MQ0=8	GT:DP	0/0:38
CH1	231	.	T	.	115.53	.	AN=2;DP=57;MQ=69.66;MQ0=8	GT:DP	0/0:36
CH1	232	.	G	.	115.53	.	AN=2;DP=57;MQ=69.66;MQ0=8	GT:DP	0/0:36
CH1	233	.	C	.	115.53	.	AN=2;DP=57;MQ=69.66;MQ0=8	GT:DP	0/0:37
CH1	234	.	A	.	139.53	.	AN=2;DP=70;MQ=59.20;MQ0=14	GT:DP	0/0:63
CH1	235	.	A	.	175.53	.	AN=2;DP=84;MQ=51.67;MQ0=15	GT:DP	0/0:79
CH1	236	.	A	.	175.53	.	AN=2;DP=84;MQ=51.67;MQ0=15	GT:DP	0/0:79
CH1	237	.	T	.	175.53	.	AN=2;DP=85;MQ=51.37;MQ0=16	GT:DP	0/0:80
CH1	238	.	A	.	175.53	.	AN=2;DP=102;MQ=46.90;MQ0=28	GT:DP	0/0:97
CH1	238	.	A	AGAAAGAAAGCTTGTA	83.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=6.172;DP=102;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=46.90;MQ0=0;MQRankSum=-6.190;QD=0.05;ReadPosRankSum=-5.733	GT:AD:DP:GQ:PL	0/1:27,25:57:99:121,0,4853
CH1	239	.	A	.	175.53	.	AN=2;DP=102;MQ=46.90;MQ0=28	GT:DP	0/0:101
CH1	240	.	T	.	175.53	.	AN=2;DP=102;MQ=46.90;MQ0=28	GT:DP	0/0:98
CH1	241	.	A	.	169.53	.	AN=2;DP=108;MQ=44.14;MQ0=29	GT:DP	0/0:107
CH1	242	.	T	.	169.53	.	AN=2;DP=109;MQ=43.94;MQ0=29	GT:DP	0/0:103
CH1	242	.	T	.	118.27	.	AN=2;DP=109;MQ=43.94;MQ0=29	GT:AD:DP	0/0:27:55
CH1	243	.	C	.	172.53	.	AN=2;DP=110;MQ=43.76;MQ0=29	GT:DP	0/0:108
CH1	243	.	CTTTT	.	118.27	.	AN=2;DP=110;MQ=43.76;MQ0=29	GT:AD:DP	0/0:27:56
CH1	244	.	T	.	91.53	.	AN=2;DP=110;MQ=43.76;MQ0=29	GT:DP	0/0:61
CH1	245	.	T	.	91.53	.	AN=2;DP=110;MQ=43.76;MQ0=29	GT:DP	0/0:53
CH1	246	.	T	.	73.53	.	AN=2;DP=110;MQ=43.76;MQ0=29	GT:DP	0/0:41
CH1	247	.	T	.	91.53	.	AN=2;DP=110;MQ=43.76;MQ0=29	GT:DP	0/0:46
CH1	248	.	A	.	172.53	.	AN=2;DP=116;MQ=42.61;MQ0=31	GT:DP	0/0:100
CH1	249	.	A	.	172.53	.	AN=2;DP=116;MQ=42.61;MQ0=31	GT:DP	0/0:100
CH1	250	.	T	.	172.53	.	AN=2;DP=117;MQ=42.43;MQ0=32	GT:DP	0/0:101
CH1	251	.	T	.	169.53	.	AN=2;DP=117;MQ=42.43;MQ0=32	GT:DP	0/0:96
CH1	251	.	T	.	118.27	.	AN=2;DP=117;MQ=42.43;MQ0=32	GT:AD:DP	0/0:27:56
CH1	252	.	C	.	172.53	.	AN=2;DP=117;MQ=42.43;MQ0=32	GT:DP	0/0:113
CH1	253	.	C	.	172.53	.	AN=2;DP=117;MQ=42.43;MQ0=32	GT:DP	0/0:110
CH1	254	.	T	.	172.53	.	AN=2;DP=117;MQ=42.43;MQ0=32	GT:DP	0/0:111
CH1	255	.	T	.	172.53	.	AN=2;DP=117;MQ=42.43;MQ0=32	GT:DP	0/0:111
CH1	256	.	T	.	172.53	.	AN=2;DP=117;MQ=42.43;MQ0=32	GT:DP	0/0:111

Line 1 is a SNP
Lines 14 and 15 are an indel that I do understand
Lines 19 and 20 I do /not/ understand
Lines 21 and 22 I do /not/ understand
---------------------------------------------------

Tags: gatk, indel, vcf

Torst

Senior Member

Join Date: Apr 2008

Posts: 275
- Share
- Tweet
#2

06-06-2013, 12:38 AM

Darren, maybe you should re-post with the lines numbered. You can use the Unix "nl" command to do this.
Comment

Previous template Next

Reply to Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems

by mylaser

Kheloyar – Everything You Need to Know About Kheloyaar Login and Kheoyar Id
If you are looking for an online gaming platform that offers a user-friendly experience, Kheloyar has become a name that many users search for. Whether you're interested in creating a new account, accessing your dashboard through Kheloyaar Login, or learning how to obtain a Kheoyar Id, understanding the platform's features and account process is essential.
This guide explains everything you need to know about...
- Channel: Articles
Today, 01:13 AM
Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems

by SEQadmin2

Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...
- Channel: Articles
07-09-2026, 11:10 AM
Cancer Drug Resistance: The Lingering Barrier to Rising Survival

by SEQadmin2

Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
- Channel: Articles
07-08-2026, 05:17 AM

Topics	Statistics	Last Post
New Analysis Splits Leukemia Into 16 Epigenomic Subgroups by SEQadmin2 Started by SEQadmin2, 07-09-2026, 10:04 AM	0 responses 11 views 0 reactions	Last Post by SEQadmin2 07-09-2026, 10:04 AM
Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2 Started by SEQadmin2, 07-08-2026, 10:08 AM	0 responses 9 views 0 reactions	Last Post by SEQadmin2 07-08-2026, 10:08 AM
Engineered Protein Motor Takes Its First Steps Along DNA Track by SEQadmin2 Started by SEQadmin2, 07-07-2026, 11:05 AM	0 responses 18 views 0 reactions	Last Post by SEQadmin2 07-07-2026, 11:05 AM
High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2 Started by SEQadmin2, 07-02-2026, 11:08 AM	0 responses 31 views 0 reactions	Last Post by SEQadmin2 07-02-2026, 11:08 AM

Unconfigured Ad

VCF Indel encoding question

Comment

Latest Articles

ad_right_rmr

News