Question: 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:

# 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 software error sequencing • 351 views
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Entering edit mode
12 months ago
zhao03 ▴ 50

after combination, the vcf file get smaller than original. those warning are ok?

-rw-rw-r-- 1 zjj zjj 5431 Apr 9 16:24 normal1.vcf.gz (original file)

-rw-rw-r-- 1 zjj zjj 32 Apr 9 16:24 normal1.vcf.gz.stats

-rw-rw-r-- 1 zjj zjj 105 Apr 9 16:24 normal1.vcf.gz.tbi

-rw-rw-r-- 1 zjj zjj 3415 Apr 8 15:32 normal.metrics

-rw-rw-r-- 1 zjj zjj 100650740 Apr 8 15:32 normal.sorted.rmdup.bam

-rw-rw-r-- 1 zjj zjj 73042319 Apr 9 16:17 normal.sorted.rmdup.reordered.bam

-rw-rw-r-- 1 zjj zjj 1128 Apr 9 16:20 normal.sorted.rmdup.reordered.bam.bai

drwx------ 19617 zjj zjj 937984 Apr 10 09:11 pon_db

-rw-rw-r-- 1 zjj zjj 1739 Apr 10 10:42 pon.vcf.gz (after CreateSomaticPanelOfNormals)

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