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Regarding different genotype calls for same sample using Unified Genotyper & Haplotype Caller

tahseentahseen IGIB,New DelhiMember

Hello Team,

I am doing multi sample cohort exome analysis for which i have called SNPs using both callers (UG & HC).For one of my important SNP, i am observing different genotypes in few samples from both the callers.
Which to rely upon for further analysis???

I am posting genotype calls for one of my SNP from both the callers along with the sampleid. Kindly have a look

caller #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67
haplotype caller 19 54311090 rs11084300 C T 5645.25 . AC=51;AF=0.464;AN=110;BaseQRankSum=1.35;ClippingRankSum=0.00;DB;DP=328;ExcessHet=0.0210;FS=10.016;InbreedingCoeff=0.2385;MLEAC=56;MLEAF=0.509;MQ=52.00;MQRankSum=-1.559e+00;QD=24.54;ReadPosRankSum=0.00;SOR=2.200 GT:AD:DP:GQ:PL ./.:0,0:0:.:0,0,0 1/1:0,4:4:12:147,12,0 0/1:4,3:7:85:85,0,111 ./.:0,0:0:.:0,0,0 1/1:0,11:11:33:373,33,0 1/1:0,9:9:27:320,27,0 1/1:0,2:2:6:71,6,0 0/0:1,0:1:3:0,3,11 0/1:3,6:9:63:180,0,63 1/1:0,5:5:15:173,15,0 0/0:6,0:6:0:0,0,29 0/0:4,0:4:12:0,12,103 0/1:2,6:8:41:193,0,41 0/0:7,0:7:21:0,21,222 0/0:2,0:2:6:0,6,48 1/1:0,2:2:6:72,6,0 ./.:0,0:0:.:0,0,0 1/1:0,7:7:21:261,21,0 0/0:5,0:5:15:0,15,140 1/1:0,6:6:18:203,18,0 1/1:0,10:10:30:317,30,0 1/1:0,15:15:45:484,45,0 1/1:0,11:11:33:357,33,0 0/0:4,0:4:9:0,9,135 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 0/0:9,0:9:27:0,27,281 0/1:3,3:6:62:62,0,85 0/0:6,0:6:18:0,18,214 1/1:0,2:2:6:66,6,0 0/1:3,6:9:66:184,0,66 1/1:0,12:12:36:425,36,0 0/0:8,0:8:24:0,24,262 0/0:3,0:3:9:0,9,77 0/1:2,4:6:46:123,0,46 ./.:0,0:0:.:0,0,0 1/1:0,4:4:12:143,12,0 0/0:2,0:2:0:0,0,1 0/0:3,0:3:0:0,0,27 1/1:0,6:6:18:210,18,0 0/0:3,0:3:9:0,9,90 0/0:3,0:3:9:0,9,98 0/1:6,2:8:45:45,0,176 0/1:4,2:6:50:50,0,122 0/1:1,3:4:20:92,0,20 0/0:4,0:4:12:0,12,120 0/1:1,2:3:21:62,0,21 0/0:4,0:4:0:0,0,60 0/0:1,0:1:3:0,3,24 1/1:0,3:3:9:106,9,0 0/0:5,0:5:0:0,0,101 ./.:0,0:0:.:0,0,0 ./.:2,0:2:.:0,0,0 0/0:4,0:4:0:0,0,66 0/1:3,3:6:73:83,0,73 0/0:6,0:6:18:0,18,188 0/1:2,5:7:47:152,0,47 ./.:1,0:1:.:0,0,0 0/1:3,5:8:70:152,0,70 0/1:5,5:10:99:143,0,116 0/0:3,0:3:0:0,0,31 ./.:0,0:0:.:0,0,0 1/1:0,9:9:27:312,27,0 ./.:0,0:0:.:0,0,0 0/1:6,7:13:99:170,0,163 ./.:0,0:0:.:0,0,0 1/1:0,2:2:6:68,6,0
unified genotyper 19 54311090 rs11084300 C T 5781.53 . AC=61;AF=0.526;AN=116;BaseQRankSum=11.126;DB;DP=342;Dels=0.00;ExcessHet=0.2545;FS=0.000;HaplotypeScore=0.2680;InbreedingCoeff=0.1031;MLEAC=62;MLEAF=0.534;MQ=53.53;MQ0=0;MQRankSum=-9.532;QD=23.99;ReadPosRankSum=0.877;SOR=0.704 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:1,4:5:12:144,12,0 0/1:4,3:7:84:84,0,110 ./.:.:.:.:. 1/1:0,11:11:33:369,33,0 1/1:0,9:9:27:315,27,0 1/1:0,2:2:6:70,6,0 0/0:1,0:1:3:0,3,33 0/1:3,6:9:63:178,0,63 1/1:0,5:5:15:171,15,0 0/1:3,3:6:49:49,0,90 0/0:4,0:4:12:0,12,130 0/1:2,7:9:38:221,0,38 0/0:8,0:8:24:0,24,265 0/0:4,0:4:12:0,12,130 1/1:0,2:2:6:70,6,0 ./.:.:.:.:. 1/1:0,7:7:21:256,21,0 0/0:7,0:7:21:0,21,221 1/1:0,6:6:18:200,18,0 1/1:0,10:10:27:304,27,0 1/1:0,15:15:42:469,42,0 1/1:0,11:11:30:343,30,0 0/0:4,0:4:12:0,12,125 ./.:.:.:.:. ./.:.:.:.:. 0/0:9,0:9:27:0,27,283 0/1:4,3:7:52:52,0,115 0/0:9,0:9:27:0,27,277 1/1:0,2:2:6:66,6,0 0/1:3,6:9:66:181,0,66 1/1:0,14:14:36:419,36,0 0/0:8,0:8:24:0,24,260 0/0:4,0:4:12:0,12,112 0/1:2,4:6:46:121,0,46 ./.:.:.:.:. 1/1:0,4:4:12:141,12,0 0/1:1,1:2:25:25,0,26 0/1:2,1:3:24:24,0,54 1/1:0,6:7:18:207,18,0 0/0:3,0:3:9:0,9,97 0/0:3,0:3:9:0,9,97 0/1:6,2:8:45:45,0,173 0/1:4,2:6:50:50,0,120 0/1:1,3:4:20:91,0,20 0/0:4,0:4:12:0,12,121 0/1:1,2:3:21:61,0,21 0/1:3,1:4:21:21,0,84 0/0:1,0:1:3:0,3,27 1/1:0,3:3:9:105,9,0 0/1:4,1:5:18:18,0,118 ./.:.:.:.:. 0/1:1,1:2:27:29,0,27 0/1:3,1:4:21:21,0,86 0/1:3,3:6:73:82,0,73 0/0:6,0:6:18:0,18,190 0/1:2,5:7:47:150,0,47 1/1:0,1:1:3:33,3,0 0/1:3,5:8:70:149,0,70 0/1:5,5:10:99:144,0,113 0/1:2,1:3:24:24,0,57 0/0:1,0:1:3:0,3,32 1/1:0,9:9:27:308,27,0 ./.:.:.:.:. 0/1:6,7:13:99:167,0,164 ./.:.:.:.:. 1/1:0,2:2:6:68,6,0

If you notice, my sampleid's 11,38,39,48,51,53,54,58,61,62 are having discordant genotypes in both callers

**Commands used for Haplotype caller **

For generating g,vcf
java -jar GenomeAnalysisTK.jar \
-R reference.fasta \
-T HaplotypeCaller \
-I sample1.bam \
--emitRefConfidence GVCF \
[--dbsnp dbSNP.vcf] \
[-L targets.interval_list] \
-o output.raw.snps.indels.g.vcf

& then combining g.vcf using GenotypeGVCFs tool (all default parameters)

Command used for unified genotyper

java -jar GenomeAnalysisTK.jar \
-R reference.fasta \
-T UnifiedGenotyper \
-I sample1....67.bam \
-stand_call_conf 40.0 \
--dbsnp dbSNP.vcf\
-L targets.interval_list]\
-o output.vcf

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