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Is that "WARN DepthPerSampleHC and WARN StrandBiasBySample" normal ?

javisjavis Member
edited April 13 in Ask the GATK team

This is my all script:

fa=/share/share/data/NGS/ref_index/GATK_bundle/hg38/Homo_sapiens_assembly38.fasta
sample=P_4
bwa mem -t 6 -M -Y -R "@RG\tID:id_${sample}\tLB:human_lib\tPL:ILLUMINA\tSM:${sample}" $fa ${sample}_1.fq.gz ${sample}_2.fq.gz | samtools view -Sb [email protected] 6 - > ${sample}.bam
samtools sort [email protected] 6 -m 4G -O bam -o ${sample}.sorted.bam ${sample}.bam
gatk MarkDuplicates -I ${sample}.sorted.bam  -O ${sample}.sorted.markup.bam  -M ${id}.metrics
samtools index [email protected] 6 ${sample}.sorted.markup.bam
gatk HaplotypeCaller -emit-ref-confidence GVCF -R $fa -I ${sample}.sorted.markdup.BQSR.bam -O ${sample}.HC.g.vcf.gz

but the output vcf shows a lot of 'WARN DepthPerSampleHC and WARN StrandBiasBySample'

17:56:20.813 WARN  DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
17:56:20.814 WARN  StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
17:56:20.922 WARN  DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
17:56:20.922 WARN  StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
17:56:20.923 WARN  DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
17:56:20.923 WARN  StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
17:56:23.635 WARN  DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
17:56:23.636 WARN  StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
17:56:23.819 WARN  DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
17:56:23.819 WARN  StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
17:56:30.539 INFO  ProgressMeter -       chr14:86514727             11.7                357050          30463.4
17:56:34.730 WARN  DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
17:56:34.730 WARN  StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
17:56:40.550 INFO  ProgressMeter -       chr14:88013743             11.9                363520          30580.1

it is pretty strange if I remove the paramter '-emit-ref-confidence GVCF' (don't use gvcf mode), it won't show the warning information. there are so many warnings, I'm afraid of getting an incorrect result.

Post edited by javis on

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