Dear all
I’m a little bit lost about differences in calling results using HaplotypeCaller or UnifiedGenotyper
I’ve a bam generated from SureSelectV5 sequencing results in Illumina
I’ve aligned following the GATK best practices protocol and I’ve recalibrated the bam

I’ve a interest region defined as
chr16 9858052 9858084
and I saved it in a file called intervals.bed

if I call using this command line

java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R References/ucsc.hg19.fasta -I xxxxx.bam -o output_uni.vcf --intervals intervals.bed -gt_mode DISCOVERY -glm BOTH

I retrieve no variants in the resulting VCF file

but if I use this command line

java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R References/ucsc.hg19.fasta -I xxxxxx.bam -o output_Haplo.vcf --intervals intervals.bed

I retrieve the following variants:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT xxxxxxxx

chr16 9858053 . CTTG C 219.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.263;ClippingRankSum=0.000;DP=94;ExcessHet=3.0103;FS=36.018;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=2.39;ReadPosRankSum=0.121;SOR=5.134 GT:AD:DP:GQ:PL 0/1:80,12:92:99:257,0,28532
chr16 9858058 . CTCTA C 207.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.658;ClippingRankSum=0.000;DP=94;ExcessHet=3.0103;FS=36.599;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=2.21;ReadPosRankSum=1.170;SOR=5.133 GT:AD:DP:GQ:PL 0/1:82,12:94:99:245,0,29822
chr16 9858064 . GGGAGCTTGATT G 195.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.011;ClippingRankSum=0.000;DP=99;ExcessHet=3.0103;FS=41.228;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=1.98;ReadPosRankSum=0.611;SOR=5.133 GT:AD:DP:GQ:PL 0/1:87,12:99:99:233,0,31151
chr16 9858079 . T TCGCCG 240.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.069;ClippingRankSum=0.000;DP=84;ExcessHet=3.0103;FS=47.853;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=2.87;ReadPosRankSum=-3.361;SOR=5.132 GT:AD:DP:GQ:PL 0/1:72,12:84:99:278,0,28511
chr16 9858081 . T A 249.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.743;ClippingRankSum=0.000;DP=82;ExcessHet=3.0103;FS=46.505;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=3.05;ReadPosRankSum=-4.304;SOR=5.132 GT:AD:DP:GQ:PL 0/1:70,12:82:99:278,0,28114
chr16 9858083 . C CATTAAAAAAAAAA 249.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.515;ClippingRankSum=0.000;DP=84;ExcessHet=3.0103;FS=46.205;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=2.97;ReadPosRankSum=-4.558;SOR=5.132 GT:AD:DP:GQ:PL 0/1:72,12:84:99:287,0,27343

Looking at this positions in IGV, it seems to agree with the UnifiedCaller. No variants

So, am I missing something ?? Is there any option I did not activate to filter out this (apparent) False Positives ??

Best Regards