the warning of GATK CreateSomaticPanelOfNormals
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Entering edit mode
12 months ago
zhao03 ▴ 50

hi, i used GATK CreateSomaticPanelOfNormals to create nomral Pon, however, there are some warnings like this:

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WARNING: No valid combination operation found for INFO field GERMQ - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MBQ - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MFRL - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MMQ - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field MPOS - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field NALOD - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field NCount - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field NLOD - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field OCM - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field PON - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field POPAF - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field ROQ - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field RPA - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field RU - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field SEQQ - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field STR - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field STRANDQ - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field STRQ - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field TLOD - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field UNIQ_ALT_READ_COUNT - the field will NOT be part of INFO fields in the generated VCF records

#
These command that i used.
java -jar /home/D/ref/gatk/gatk-package-4.1.4.1-local.jar Mutect2 \
--native-pair-hmm-threads 16 \
-R /home/D/ref/hg19/ucsc.hg19.fasta \
-I normal.sorted.rmdup.reordered.bam \
-L T086V5_CNV.igt.bed \
--max-mnp-distance 0 \
--independent-mates true \
-O normal1.vcf.gz

java -jar /home/D/ref/gatk/gatk-package-4.1.4.1-local.jar GenomicsDBImport \
-R /home/D/ref/hg19/ucsc.hg19.fasta \
-L T086V5_CNV.igt.bed \
--genomicsdb-workspace-path pon_db \
-V normal1.vcf.gz \

java -jar /home/D/ref/gatk/gatk-package-4.1.4.1-local.jar CreateSomaticPanelOfNormals -R /home/D/ref/hg19/ucsc.hg19.fasta -V gendb://pon_db -O pon.vcf.gz
SNP genome sequencing • 530 views
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