HaplotypeCaller can't find variants when using GENOTYPE_GIVEN_ALLELES?

Hello,

I want to call variants in some samples with the HaplotypeCaller using the GENOTYPE_GIVEN_ALLELES mode. I have used a vcf file with 2 variants for the -alleles option, and a bed file with regions of 100 bp around those variants. The output vcf did not contain any variants. I then tried using the HaplotypeCaller in DISCOVERY mode with only the bed file. This gave me a list of 14 variants, among which the 2 variants I was looking for. What could be the reason for the HaplotypeCaller to not find the variants when using GENOTYPE_GIVEN_ALLELES?

Here are the commands I have run:

/opt/Software/java/sun-jre-8/bin/java -jar /opt/NGS/binaries/gatk/GATK_3.6.0/GenomeAnalysisTK.jar \
    -R /opt/NGS/References/hg19/samtools/0.1.19/hg19.fasta \
    -T HaplotypeCaller \
    -I 103091_s1.dedup.real.recal.bam \
    -I 103092_s3.dedup.real.recal.bam \
    -I 103395_s2.dedup.real.recal.bam \
    -L chrY.variants.bed \
    -o chrY.output.discovery.vcf

/opt/Software/java/sun-jre-8/bin/java -jar /opt/NGS/binaries/gatk/GATK_3.6.0/GenomeAnalysisTK.jar \
    -R /opt/NGS/References/hg19/samtools/0.1.19/hg19.fasta \
    -T HaplotypeCaller \
    -I 103091_s1.dedup.real.recal.bam \
    -I 103092_s3.dedup.real.recal.bam \
    -I 103395_s2.dedup.real.recal.bam \
    --genotyping_mode GENOTYPE_GIVEN_ALLELES \
    -alleles chrY.variants.vcf \
    -L chrY.variants.bed \
    -o chrY.output.given.vcf

The content of the bed and the vcf file are:

bed file:

chrY    10,011,794  10,011,994
chrY    21,154,326  21,154,526

vcf file for -alleles (without header):

CHROM   POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  103091_s1
chrY    10011894    .   ATTAT   A   2718.73 VQSRTrancheINDEL99.00to99.90    AC=1;AF=0.500;AN=2;BaseQRankSum=1.645;ClippingRankSum=0.747;DP=375;ExcessHet=3.0103;FS=1.689;HRun=0;MLEAC=1;MLEAF=0.500;MQ=41.48;MQRankSum=0.063;QD=7.90;RPA=2,1;RU=TTAT;ReadPosRankSum=-0.129;SOR=0.815;STR;VQSLOD=-1.694e+00;culprit=MQRankSum    GT:AD:DP:GQ:PL  0/1:259,85:344:99:2756,0,10508
chrY    21154426    .   G   A   430.77  VQSRTrancheSNP99.00to99.90  AC=1;AF=0.500;AN=2;BaseQRankSum=-1.835;ClippingRankSum=-3.340;DP=28;ExcessHet=3.0103;FS=3.372;HRun=0;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-0.894;QD=15.38;ReadPosRankSum=1.082;SOR=0.486;VQSLOD=0.427;culprit=QD  GT:AD:DP:GQ:PL  0/1:11,17:28:99:459,0,313

Thanks in advance.