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HaplotypeCaller haploid GVCF format error?

Hi all,

I prepared a clean Bam file following GATK Best Practice and used GATK4 HaplotypeCaller to create a gvcf with ploidy1 option:

gatk- HaplotypeCaller --native-pair-hmm-threads 24 -I KU_filtered_sorted_mdup.bam -O HC.KU.raw.snps.indels.g.vcf -R ref.fasta -ploidy 1 --emit-ref-confidence GVCF

When I validated the gvcf, ValidateVariants threw errors at the end:

When I ran GenotypeGVCFs using the gvcf, it ran to completion, but threw the same "java.lang.IllegalArgumentException" errors at the end.

My java is Java runtime: OpenJDK 64-Bit Server VM v1.8.0_162-8u162-b12-0ubuntu0.16.04.2-b12.

Could you please help me with this problem?
Many thanks.

Best Answer


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