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Haplotype caller not picking up variants for HiSeq Runs

We were sequencing all our data in HiSeq and now moved to nextseq. We have sequenced the same batch of samples on both the sequencers. Both are processed using the same pipeline/parameters.
What I have noticed is, GATK 3.7 HC is not picking up variants, even though the coverage is good and is evidently present in the BAM file.

For example the screenshot below shows the BAM files for both NextSeq and HiSeq sample. There are atleast 3
variants in the region 22:29885560-29885861(NEPH, exon 5) that is expected to be picked up for HiSeq.

These variants are picked up for NextSeq samples (even though the coverage for hiSeq is much better).

The command that I have used for both samples is

java -Xmx32g -jar GATK_v3_7/GenomeAnalysisTK.jar -T HaplotypeCaller -R GRCh37.fa --dbsnp GATK_ref/dbsnp_138.b37.vcf -I ${i}.HiSeq_Run31.variant_ready.bam -L NEPH.bed -o ${i}.HiSeq_Run31.NEPH.g.vcf

Any idea why this can happen ?

Many thanks,


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