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Warnings in CreateSomaticPanelOfNormals after GenomicsDBImport

manolismanolis Member ✭✭
edited May 8 in Ask the GATK team

gatk 4.1.1.0, bash pipeline, linux server, WES data

Hi,

just a question considering that they are just warnings:

after GDBI tool I run the CreateSomaticPanelOfNormals tool and I have these warning messages:

07:22:15.863 INFO CreateSomaticPanelOfNormals - Initializing engine
07:22:16.381 INFO FeatureManager - Using codec VCFCodec to read file file:///shared/resources/gatk4hg38db/af-only-gnomad.hg38.vcf.gz
WARNING: No valid combination operation found for INFO field CONTQ - the field will NOT be part of INFO fields in the generated VCF records
WARNING: No valid combination operation found for INFO field ECNT - the field will NOT be part of INFO fields in the generated VCF records
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
07:22:19.336 INFO CreateSomaticPanelOfNormals - Done initializing engine
07:22:19.479 INFO ProgressMeter - Starting traversal
07:22:19.479 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
... same warnings ...
07:23:51.307 INFO ProgressMeter - chr1:1048793 1.5 1000 653.4
07:24:01.334 INFO ProgressMeter - chr1:26271182 1.7 16000 9425.2
07:24:11.697 INFO ProgressMeter - chr1:75234146 1.9 28000 14971.0
07:24:22.380 INFO ProgressMeter - chr1:154237014 2.0 41000 20016.1
07:24:32.390 INFO ProgressMeter - chr1:201209877 2.2 52000 23474.5
07:24:42.420 INFO ProgressMeter - chr1:248061119 2.4 63000 26444.5
... same warnings ...
07:25:30.031 INFO ProgressMeter - chr10:382506 3.2 64000 20152.1
07:25:40.548 INFO ProgressMeter - chr10:50050649 3.4 73000 21783.6
07:25:50.689 INFO ProgressMeter - chr10:103584776 3.5 84000 23862.5
... same warnings ...
....
....

Is it something normal (I guess that missing some data and for this I have these warnings)? Are them related to a specific genome position/variant or is something more general?

Somehow can I fix them? or those data are not important for downstream analysis (Tumor sample analysis with Mutect2+PON)?

single sample pon

${GATK4} --java-options "${javaOpt}" Mutect2 \
-R ${hg38} \
-I "${bqsr}.bam" \
-O "${sample-PON}.vcf.gz" \
-L ${wes_intervals} \
-ip ${pad} \
--max-mnp-distance "0"

cohort pon

${GATK4} --java-options "${javaOpt}" GenomicsDBImport \
-R ${hg38} \
-V ... -V ... \
-L ${chromosome_list} \
-ip ${pad} \
--batch-size 1 \
--reader-threads 1 \
--genomicsdb-workspace-path "GDBI"

${GATK4} --java-options "${javaOpt}" CreateSomaticPanelOfNormals \
-R ${hg38}
-V gendb://"GDBI" \
-O "${cohort-PON}.vcf.gz" \
--germline-resource ${AFGNOMAD}

Thanks

Answers

  • manolismanolis Member ✭✭
    edited May 8

    Here the header:

    ##fileformat=VCFv4.2
    ##GATKCommandLine=<ID=CreateSomaticPanelOfNormals,CommandLine="CreateSomaticPanelOfNormals ...
    ##INFO=<ID=BETA,Number=2,Type=Float,Description="Beta distribution parameters to fit artifact allele fractions">
    ##INFO=<ID=FRACTION,Number=1,Type=Float,Description="Fraction of samples exhibiting artifact">
    ##contig=<ID=chr1,length=248956422,assembly=38>
    ...
    ##contig=<ID=HLA-DRB1*16:02:01,length=11005,assembly=38>
    ##normal_sample=wes12928
    ...
    ##normal_sample=wesC597
    ##source=CreateSomaticPanelOfNormals
    #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
    
  • bshifawbshifaw moonMember, Broadie, Moderator admin
    edited May 12

    Chances are its removing the head for the annotations because there wasn't anything written under that column from the previous tools, but you could double check the vcf files. If you want wanted to confirm that your VCF is still valid then use ValidateVariants. And have a look at the Mutect2 tutorial on the sections regarding annotations.

    Post edited by bshifaw on
  • manolismanolis Member ✭✭
  • summerghwsummerghw Member
    @manolis ,Hi, I have the same problem with you , i use GATK 4.1.1.0 CreateSomaticPanelOfNormals
    , and have the sam WARNING , and the pon.gz.vcf only have 4K variants. Did you fix your problem ?
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