a) GATK version used: 4.1.4.1
b) Exact GATK commands used:

gatk HaplotypeCaller -I NA12878.final.cram -O NA12878.final.vcf -R GRCh38_full_analysis_set_plus_decoy_hla.fa -L vdj_hg38.bed

c) The entire error log:

java.lang.NullPointerException
at java.base/java.util.ComparableTimSort.countRunAndMakeAscending(ComparableTimSort.java:325)
at java.base/java.util.ComparableTimSort.sort(ComparableTimSort.java:202)
at java.base/java.util.Arrays.sort(Arrays.java:1315)
at java.base/java.util.Arrays.sort(Arrays.java:1509)
at java.base/java.util.ArrayList.sort(ArrayList.java:1749)
at java.base/java.util.Collections.sort(Collections.java:145)
at org.broadinstitute.hellbender.utils.IntervalUtils.sortAndMergeIntervals(IntervalUtils.java:492)
at org.broadinstitute.hellbender.utils.IntervalUtils.getIntervalsWithFlanks(IntervalUtils.java:990)
at org.broadinstitute.hellbender.utils.IntervalUtils.getIntervalsWithFlanks(IntervalUtils.java:1005)
at org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.<init>(MultiIntervalLocalReadShard.java:59)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.makeReadShards(AssemblyRegionWalker.java:104)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.onStartup(AssemblyRegionWalker.java:84)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)

I used HaplotypeCaller on the cram file of sample NA12878 from IGSR, the reference fasta is also downloaded from them, the bed interval is self-made (tab delimited). I have tried to run HaplotypeCaller with no -L, or -L with manual input, it works fine

chr1    47264754    47264933
chr1    47276480    47276621
chr1    47276812    47276856
chr1    47278168    47278295
chr1    47279154    47279278
chr1    47279581    47279735
chr1    47279881    47279987
chr10   135345089   135345238
chr10   135345628   135345788
chr10   135346196   135346372
chr10   135347260   135347401
chr10   135350567   135350754
chr10   135351255   135351396
chr10   135352284   135352468

Could you please help me on what have gone wrong?

Edit: summary of what I have tried:

• Used another bed file, contain intervals from chr1 to chr9: work
• Used another bed file, contain intervals from chr10: NOT work
• Used another bed file, contain intervals from chr1 to chr10: NOT work
• Used another bed file, contain intervals from chr11 to chr19: work
• Used another bed file, contain intervals from chr11 to chr22: NOT work
• Used another bed file, contain intervals from chr1 to chr9 and chr11 to chr19: work