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Published
20 hours ago •
google
google
Homozygous GT value while IGV shows otherwise
Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6.1/docs/FAQ.md: Yes Describe the issue: Although some variants are clearly heterozygous in IGV, deepvariant GT shows a homozygous genotype.
Setup
- Operating system: linux
- DeepVariant version: 1.6.1
- Installation method : Docker
- Type of data: illumina, WES, hg38
Steps to reproduce:
docker run --rm -i \
-v ${ref_dir}:/opt/ref \
-v ${kit_dir}:/opt/kit \
-v ${input_dir}:/opt/sample \
${deepvariant_docker} \
/opt/deepvariant/bin/run_deepvariant \
--model_type=WES \
--ref="/opt/ref/${ref_fasta}" \
--reads="/opt/sample/${input_bam_file}" \
--regions="/opt/kit/${kit_bed_file}" \
--output_vcf="/opt/sample/${input_bam_file/.bam/.dv.vcf}" \
--num_shards="${threads}"
Here are 5 selected variants called by 5 different versions of deepvariant:
v0.10.0 chr12 11353713 . T C 57.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:54:43:27,15:0.348837:57,0,55
v1.1.0 chr12 11353713 . T C 36.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:34:44:28,15:0.340909:36,0,38
v1.4.0 chr12 11353713 . T C 23.3 PASS . GT:GQ:DP:AD:VAF:PL 0/1:21:44:28,15:0.340909:23,0,25
v1.5.0 chr12 11353713 . T C 24.3 PASS . GT:GQ:DP:AD:VAF:PL 0/1:17:44:28,15:0.340909:24,0,17
v1.6.1 chr12 11353713 . T C 24.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:5:44:28,15:0.340909:22,3,0
-----------------------------
v0.10.0 chr3 195779035 . G A 3.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:4:33:24,8:0.242424:1,0,38
v1.1.0 chr3 195779035 . G A 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:41:33:24,8:0.242424:0,43,45
v1.4.0 chr3 195779035 . G A 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:23:33:24,8:0.242424:0,32,22
v1.5.0 chr3 195779035 . G A 0.1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:16:33:24,8:0.242424:0,26,16
v1.6.1 chr3 195779035 . G A 13.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:14:33:24,8:0.242424:13,28,0
-----------------------------
v0.10.0 chr6 159711482 . C T 46.5 PASS . GT:GQ:DP:AD:VAF:PL 0/1:36:70:38,32:0.457143:46,0,36
v1.1.0 chr6 159711482 . C T 6.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:7:80:46,34:0.425:5,0,20
v1.4.0 chr6 159711482 . C T 1.8 RefCall . GT:GQ:DP:AD:VAF:PL ./.:5:80:46,34:0.425:0,3,9
v1.5.0 chr6 159711482 . C T 2.3 RefCall . GT:GQ:DP:AD:VAF:PL ./.:4:80:46,34:0.425:0,2,8
v1.6.1 chr6 159711482 . C T 9.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:3:80:46,34:0.425:6,0,0
-----------------------------
v0.10.0 chr14 106592660 . G A 64.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:59:93:38,55:0.591398:64,0,60
v1.1.0 chr14 106592660 . G A 30.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:8:95:38,57:0.6:29,6,0
v1.4.0 chr14 106592660 . G A 4.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:3:95:38,57:0.6:1,0,5
v1.5.0 chr14 106592660 . G A 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:43:95:38,57:0.6:0,44,48
v1.6.1 chr14 106592660 . G A 23.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:5:95:38,57:0.6:22,3,0
-----------------------------
v0.10.0 chr1 1668449 . A G 47.2 PASS . GT:GQ:DP:AD:VAF:PL 0/1:45:158:71,87:0.550633:47,0,49
v1.1.0 chr1 1668449 . A G 23.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:7:164:75,89:0.542683:22,0,5
v1.4.0 chr1 1668449 . A G 40 PASS . GT:GQ:DP:AD:VAF:PL 1/1:32:164:75,89:0.542683:40,32,0
v1.5.0 chr1 1668449 . A G 41.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:31:164:75,89:0.542683:41,31,0
v1.6.1 chr1 1668449 . A G 43.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:29:164:75,89:0.542683:43,28,0
As you can see specially in 1.6.1 the genotype is GT:1/1 while earlier versions were GT:0/1
