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GenotypeGVCF missing some genotype call

wlaiwlai Member
edited March 2019 in Ask the GATK team
Hi, i am doing an analysis on exome sequencing with 31 samples following best practices.

-HaplotypeCaller:
java1.8 -Xmx10g -jar $gatk_jar HaplotypeCaller --native-pair-hmm-threads 20 -R $reference_dir -I ${SAMPLENAME}_bqsr.bam -O ${SAMPLENAME}.g.vcf.gz --genotyping-mode DISCOVERY -ERC GVCF

-Genomics DB:
less target.list| while read line ; do gatk --java-options -DGATK_STACKTRACE_ON_USER_EXCEPTION=true GenomicsDBImport --genomicsdb-workspace-path diabetes_DB_$line -L $line --sample-name-map LB_map --batch-size 50 --tmp-dir tmp --reader-threads 5 ; done

-GenotypeGVCFs:
gatk GenotypeGVCFs -R /home/Graceca/references/hs38/hs38DH.fa -V gendb://diabetes_DB_chr9:3824126-4310693 -O test_out.vcf.gz --tmp-dir ./tmp

-some output :
15:56:21.275 INFO GenotypeGVCFs - GCS max retries/reopens: 20
15:56:21.275 INFO GenotypeGVCFs - Requester pays: disabled
15:56:21.275 INFO GenotypeGVCFs - Initializing engine
WARNING: No valid combination operation found for INFO field DS - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field DS - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records
15:56:22.246 INFO GenotypeGVCFs - Done initializing engine
15:56:22.304 INFO ProgressMeter - Starting traversal
15:56:22.304 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
WARNING: No valid combination operation found for INFO field DS - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records
15:56:23.354 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples
15:56:23.411 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples
15:56:23.629 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples
15:56:23.631 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples
15:56:23.646 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples
15:56:23.743 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples
15:56:23.770 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples
15:56:23.809 WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples


This is the output of 31 gcvf files:

chr9 3836809 . C A 11.03 . AC=2;AF=0.067;AN=30;DP=38;ExcessHet=0.0755;FS=0.000;InbreedingCoeff=0.2923;ML
EAC=1;MLEAF=0.033;MQ=60.00;QD=5.51;SOR=0.693 GT:AD:DP:GQ:PL ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 0/0:5,0:5:15:0,15,
109 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 0/0:2,0:2:6:0,6,38 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0
:0:.:0,0,0 0/0:2,0:2:6:0,6,37 ./.:0,0:0:.:0,0,0 0/0:2,0:2:6:0,6,39 0/0:2,0:2:6:0,6,37 ./.:0,0:0:.:0,0,0
0/0:1,0:1:3:0,3,14 1/1:0,2:2:6:49,6,0 0/0:2,0:2:6:0,6,37 ./.:0,0:0:.:0,0,0 0/0:2,0:2:6:0,6,43 0/0:2,
0:2:6:0,6,37 0/0:2,0:2:6:0,6,39 0/0:5,0:5:15:0,15,114 0/0:2,0:2:6:0,6,39 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0
0/0:4,0:4:12:0,12,79 0/0:3,0:3:9:0,9,59 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,
0:0:.:0,0,0

Some sample has no annotation at all. May i know what causes that?
Post edited by wlai on
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