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@bhanuGandham Thank you for your help!
@Bhanu command: gatk HaplotypeCaller \ -R ~/seqlib/melonomics/genome/genome.fa \ --emit-ref-confidence GVCF \ -I file.sorted.markdup.realign.BQSR.bam \ -O file.sorted.markdup.realign.BQSR.g.vcf tool and version is : GATK220.127.116.11 the file is t…
@Sheila when i use GenotypeGVCFs on a single single-sample GVCF gatk GenotypeGVCFs \ -R genome.fa \ -V R97.sorted.markdup.realign.BQSR.g.vcf \ -O R97.sorted.markdup.realign.BQSR.vcf I am getting the WARN "10:04:24.236 WARN ReferenceConf…
(Image) I also encountered such a problem. I want to know why this is happening.