gatk assessment follow up
DESCRIPTION
GATK assessment follow up. Jianying Li. Samples tested. Analytical parameter set up. Aligner: BWA 0.5.9 Samtools : 0.1.12a GATK: 1.0.5083 Covariates: readgroup * , Q raw , dinucleotide, machine cycle SVA version: 1.1. Reported quality score (als9c2, build 37). - PowerPoint PPT PresentationTRANSCRIPT
GATK assessment follow up
Jianying Li
Samples tested
SAMPLE Gender ETHNICITYGenome ref
AVERAGE_COVERAGE dbsnp
mchd002a2 Female Female Build 36 30.77 dbsnp_132
dukscz0106 Male Male Build 36 28.93 dbsnp_132
als9c2 Female white Build 37 41.53 v4.0
na12878 Female 1KG Build 36/7 40 dbsnp_132
Analytical parameter set up
• Aligner: BWA 0.5.9• Samtools: 0.1.12a• GATK: 1.0.5083• Covariates: readgroup*, Qraw, dinucleotide,
machine cycle• SVA version: 1.1
Reported quality score (als9c2, build 37)
Before recalibration After recalibration
15% more bases with Q32 and above
Computational complexity
SNVs & Indel files
Processed BAM files
var_flt_vcf.snpvar_flt_vcf.indel
SNV count Hom/het ratio Indel countTi/Tv ratio Overlap
with dbSNPconcordance
Het/tot ratio on X
~ 4 days
~ 6 hours
Increased variant calls (als9c2)Metrics Raw GATK -recal
All SNVs 3,668,875 3,724,498
Filtered SNVs 3,508,465 3,570,758
INDELs 521,506 521,680
All SNVs Filtered SNVs INDELs0
500000
1000000
1500000
2000000
2500000
3000000
3500000
4000000
als9c2 (raw)als9c2 (GATK)
Ratio (%) of variant calls --GATK against raw
All SNVs Filtered SNVs INDELs97.50
98.00
98.50
99.00
99.50
100.00
100.50
101.00
101.50
102.00
als9c2dukscz0106mchd002A2
Ti/Tv ratio (??)
Ti/Tv Ratio Raw GATK
mchd002a2 2.1226 2.1343
als9c2 2.1548 2.1286
dukscz0106 2.1408 2.1287
Reduced overlap to dbsnp
Overlap dbsnp autosomes Samtools.1.12 GATK
na12878 (1000G) 95.27 running..
mchd002a2 89.32 89.06
als9c2 93.2 93.05
dukscz0106 83.13 82.2
Increased concordance (SVA)
part_I matched no.matched match%
Part I gatk 294629 3018 98.9860
raw 293658 3039 98.9757
Part II gatk 280499 6629 97.6913
raw 280504 7591 97.3651
Over all gatk 575128 9647 98.3503
raw 574162 10630 98.1823
Dukscz0106, build 36
match%_partI match%_partII Overall0.965
0.97
0.975
0.98
0.985
0.99
0.995
gatkraw
Increased concordance (SVA)
als9c2, build 37
part_I matched no.matched match%
Part I gatk 296497 1297 99.5645
raw 294755 1842 99.3790
Part II gatk 281392 3882 98.6392
raw 281402 5365 98.1291
Overall gatk 577889 5179 99.1118
raw 576157 7207 98.7646
match%_partI match%_partII Overall0.97
0.975
0.98
0.985
0.99
0.995
1
als9c2-gatkals9c2-raw
Decreased concordance (??)
mchd002A2, build 36
part_I matched no.matched match%
Part I gatk 299325 1026 99.6584
raw 300054 984 99.6731
Part II gatk 281392 3882 98.6392
raw 280139 3675 98.7051
Over all gatk 280494 3265 98.8494
raw 580193 4659 99.2034
match%_partI match%_partII Overall%0.982
0.984
0.986
0.988
0.99
0.992
0.994
0.996
0.998
mchd002A2-gatkmchd002A2-raw