We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

Is that "WARN DepthPerSampleHC and WARN StrandBiasBySample" normal ?

javisjavis Member
edited April 2019 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

Best Answers

Answers

Sign In or Register to comment.