GATK v4.0.11.0 & v4.1.0.0, linux server, bash
Hi,
I was running the following codes
${GATK4} --java-options '-Xmx10g -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:ConcGCThreads=1 -XX:ParallelGCThreads=2' HaplotypeCaller -R /shared/resources/hgRef/hg38/Homo_sapiens_assembly38.fasta -I /home/manolis/GATK4/2.BQSR/bqsr_PROVA/WES_16-1239_bqsr.bam -O "PROVA_${version}.g.vcf.gz" -L /home/manolis/GATK4/DB/hg38_SureSelectV6noUTR_S07604514_HC_1-22_XY.intervals -ip 100 -ERC GVCF --max-alternate-alleles 3 -ploidy 2 -A StrandBiasBySample --tmp-dir /home/manolis/GATK4/tmp/
${GATK4} --java-options '-Xmx10g -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:ConcGCThreads=1 -XX:ParallelGCThreads=2' ValidateVariants -R /shared/resources/hgRef/hg38/Homo_sapiens_assembly38.fasta -V "PROVA_${version}.g.vcf.gz" -L/home/manolis/GATK4/DB/hg38_SureSelectV6noUTR_S07604514_HC_1-22_XY.intervals -ip 100 -gvcf -Xtype ALLELES --tmp-dir /home/manolis/GATK4/tmp/
and I created the following files:
HaplotypeCaller v4.0.11.0 -> output "PROVA_v40110.g.vcf.gz"
HaplotypeCaller v4.1.0.0 -> output "PROVA_v4100.g.vcf.gz"
When I'm going to validate them I have the following results:
1) ValidateVariants v4.0.11.0 -> input "PROVA_v40110.g.vcf.gz" ........ Everything OK !!!
2) ValidateVariants v4.0.11.0 -> input "PROVA_v4100.g.vcf.gz" ........ Everything OK !!!
3) ValidateVariants v4.1.0.0 -> input "PROVA_v4100.g.vcf.gz" ........ ERROR !!!
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A USER ERROR has occurred: In a GVCF all records must ordered. Record: [VC Unknown @ chr2:41350-41765 Q. of type=SYMBOLIC alleles=[A*, <NON_REF>] attr={END=41765} filters= covers a position previously traversed.
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4) ValidateVariants v4.1.0.0 -> input "PROVA_v40110.g.vcf.gz" ........ ERROR !!!
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A USER ERROR has occurred: In a GVCF all records must ordered. Record: [VC Unknown @ chr2:41350-41765 Q. of type=SYMBOLIC alleles=[A*, <NON_REF>] attr={END=41765} filters= covers a position previously traversed.
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If I create a vcf.gz file with HaplotypeCaller v4.1.0.0 (standard mode, NO gVCF ) and I'm going to validate it with ValidateVariants v4.1.0.0 I do not have any error!
For now... can I Validate my g.vcf.gz files generated from HC v4.1.0.0 with ValidateVariants of the v4.0.11.0?
Thanks