Process ASE_KNOWNSNPS (SAMPLE123XYZ) terminated with an error exit status (2) (More then one variant context at position: chr3:XXXXXXX)

[SINGHVJ-Bio]

No description provided.

[SINGHVJ-Bio]

I am getting following error .....
Note: I verified input vcf file, and there are no duplicate SNPs observed.
[July 7, 2022 7:40:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter done. Elapsed time: 4.55 minutes.
Runtime.totalMemory()=2552233984

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A USER ERROR has occurred: More then one variant context at position: chr3:10992891

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Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Using GATK jar /home/name/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar defined in environment variable GATK_LOCAL_JAR
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 /home/name/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar ASEReadCounter -R Homo_sapiens_assembly38_1-22_X.fasta -O ASE.tsv -I SAMPLE123XYZ.final.uniq.bam -V known_snps.vcf.gz

[SINGHVJ-Bio]

Looks like a GATK ASEReadCounter problem, so replaced following in modules.nf

gatk ASEReadCounter
-R ${genome}
-O ASE.tsv
${bam_params}
-V ${vcf}

The new code added as ...

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 /home/name/GenomeAnalysisTK-3.8/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar
-T ASEReadCounter
-R ${genome}
-o ASE.tsv
${bam_params}
-sites ${vcf}

The GenomeAnalysisTK.jar file downloaded from following link
GenomeAnalysisTK.jar

@pditommaso, please check and update if ok