Somehow the requested coordinate is not covered by the read?

I was running some samtools calls through UG with genotyping_mode GENOTYPE_GIVEN_ALLELES after reading this thread:

http://gatkforums.broadinstitute.org/discussion/1842/variant-annotator-not-annotating-mappingqualityranksumtest-and-readposranksumtest-for-indels

I got this error message:

##### ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Alignment 440969 | 36S26M1D6M1I2M1D1M3D27M1S

What did I do wrong? It works for most other fragments (chrom20:pos1-pos2). Is it possible to avoid this error message and just do ./. calls at coordinates not covered by reads? I'm not sure, why samtools called at a coordinate not covered by a read. I don't know at which coordinate this happened. I was at this coordinate, when the error happened:

INFO  10:21:06,036 ProgressMeter -       20:479014   2329564.0    55.0 m      23.6 m        0.6%     6.7 d       6.7 d 

I was using this command:

vcf=samtools.vcf.gz
$java -Djava.io.tmpdir=tmp -Xmx63900m \
 -jar $jar \
 --analysis_type UnifiedGenotyper \
 --reference_sequence $ref \
 --input_file bam.list \
 --dbsnp $dbsnp138 \
 --num_cpu_threads_per_data_thread 3 \
 --num_threads 4 \
 --out $out \
 --intervals $vcf \
 -stand_call_conf 10 \
 -stand_emit_conf 10 \
 --genotype_likelihoods_model BOTH \
 --output_mode EMIT_ALL_SITES \
 --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest \
 --alleles $vcf \
 --genotyping_mode GENOTYPE_GIVEN_ALLELES \
 -L 20:$pos1-$pos2 \