not all sites emitted with GENOTYPE_GIVEN_ALLELES

I am running HC3.3-0 with the following options (e.g. GENOTYPE_GIVEN_ALLELES):

$java7 -Djava.io.tmpdir=tmp -Xmx3900m \
 -jar $jar \
 --analysis_type HaplotypeCaller \
 --reference_sequence $ref \
 --input_file $BAM \
 --intervals $CHROM \
 --dbsnp $dbSNP \
 --out $out \
 -stand_call_conf 0 \
 -stand_emit_conf 0 \
 -A Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest \
 -L $allelesVCF \
 -L 20:60000-70000 \
 --interval_set_rule INTERSECTION \
 --genotyping_mode GENOTYPE_GIVEN_ALLELES \
 --alleles $allelesVCF \
 --emitRefConfidence NONE \
 --output_mode EMIT_ALL_SITES \

The file $allelesVCF contains these neighbouring SNPs:

20  60807   .   C   T   118.96  .
20  60808   .   G   A   46.95   .
20  61270   .   A   C   2870.18 .
20  61271   .   T   A   233.60  .

I am unable to call these neighbouring SNPs; despite reads being present in the file $BAM, which shouldn't matter anyway. I also tried adding --interval_merging OVERLAPPING_ONLY to the command line, but that didn't solve the problem. What am I doing wrong? I should probably add GATK breaker/misuser to my CV...

Thank you as always.

P.S. The CommandLineGATK documentation does not say, what the default value for --interval_merging is.

P.P.S. Iterative testing a bit slow, because HC always has to do this step:

HCMappingQualityFilter - Filtering out reads with MAPQ < 20