If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: gatk-4.1.8.1
b) Exact command used: gatk GenotypeConcordance -TRUTH_VCF new.vcf.gz -TRUTH_SAMPLE 0_fam0110_G110 -CALL_SAMPLE 0_fam0110_G110 -CALL_VCF old.vcf.gz -O concordance.vcf -OUTPUT_VCF true
c) Entire error log:

Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /software/linux-el7-x86_64/apps/gatk-4.1.8.1/gatk/build/gatk-4.1.8.1-32-g6018c7b-SNAPSHOT/gatk-package-4.1.8.1-32-g6018c7b-SNAPSHOT-local.jar GenotypeConcordance -TRUTH_VCF new.vcf.gz -TRUTH_SAMPLE 0_fam0110_G110 -CALL_SAMPLE 0_fam0110_G110 -CALL_VCF old.vcf.gz -O concordance.vcf -OUTPUT_VCF true
12:03:02.832 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/software/linux-el7-x86_64/apps/gatk-4.1.8.1/gatk/build/gatk-4.1.8.1-32-g6018c7b-SNAPSHOT/gatk-package-4.1.8.1-32-g6018c7b-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Sep 16 12:03:02 CDT 2020] GenotypeConcordance --TRUTH_VCF new.vcf.gz --CALL_VCF old.vcf.gz --OUTPUT concordance.vcf --OUTPUT_VCF true --TRUTH_SAMPLE 0_fam0110_G110 --CALL_SAMPLE 0_fam0110_G110 --INTERSECT_INTERVALS true --MIN_GQ 0 --MIN_DP 0 --OUTPUT_ALL_ROWS false --USE_VCF_INDEX false --MISSING_SITES_HOM_REF false --IGNORE_FILTER_STATUS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
Sep 16, 2020 12:03:03 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
[Wed Sep 16 12:03:03 CDT 2020] Executing as anamaria@login-1.saber.acer.uic.edu on Linux 3.10.0-693.21.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_161-b14; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.8.1-32-g6018c7b-SNAPSHOT
[Wed Sep 16 12:03:03 CDT 2020] picard.vcf.GenotypeConcordance done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2209873920
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequences at index 0 don't match: 0/249139234/1 0/249218993/1
at htsjdk.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:272)
at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:334)
at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:320)
at picard.vcf.GenotypeConcordance.doWork(GenotypeConcordance.java:344)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:301)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)

If not an error, choose a category for your question(REQUIRED):
a)How do I (......)?
b) What does (......) mean?

Can you please tell me how to resolve this issue? Om the same set of files I was able to run this without error:

gatk Concordance -R human_g1k_v37.fasta -eval new.vcf.gz --truth old.vcf.gz --summary summary.tsv

Can you please tell m
c) Why do I see (......)?
d) Where do I find (......)?
e) Will (......) be in future releases?