VCF Indel encoding question

[darren.obbard]

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

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

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

[Torst]

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