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What is PL 0,0?

I have a genomics data from Bacteria (E. Coli.) and used GATK 4 for variant calling. I have noticed that for some samples and some loci, PL is 0,0. Can anyone please explain this?

eg. NC_000913 4473651 . C . . . GT:AD:DP:GQ:PL 0:2,0:2:0:0,0

How can we interpret that? becuase in this case, the GT in later steps will be "." as it will be driven from PL, when we combine and genotype the samples.

thanks in advance.

Answers

  • akovalskakovalsk Member, Broadie, Moderator admin
    edited September 13

    Hi @Negin could you please share the header of the VCF, as well as the tools and exact commands that were used and version of GATK?

  • NeginNegin Member

    Hi @akovalsk, this is the header of my file:

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE

    As I mentioned, I used GATK version 4.1.1.0 for variant calling and BP_Resolutiin.

  • akovalskakovalsk Member, Broadie, Moderator admin

    Hi @Negin my apologies, let me clarify: We need to see the entire header of the VCF file, including any fields starting with a "#" (so the full list of the lines that start ##INFO, ##FILTER, etc).

    Could you also provide the exact command you used when running the tools in question? We will need to know which exact tool was used with which exact additional arguments.

  • NeginNegin Member

    Hi @akovalsk,
    Here is the header of my file:

    fileformat=VCFv4.2

    ALT=<ID=NON_REF,Description="Represents any possible alternative allele at thi

    s location">

    FILTER=<ID=LowQual,Description="Low quality">

    FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref an

    d alt alleles in the order listed">

    FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads

    with MQ=255 or with bad mates are filtered)">

    FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">

    FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

    FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled like

    lihoods for genotypes as defined in the VCF specification">

    FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statisti

    cs which comprise the Fisher's Exact Test to detect strand bias.">

    GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --sample-plo

    idy 1 --emit-ref-confidence BP_RESOLUTION --output bp-r
    esolution/Autumn_2013_ALT_17.g.vcf.gz --input reference.fna --use-new-qual-calculator true --use-old-qu
    al-calculator false --annotate-with-num-discovered-alleles false --heterozygosit
    y 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-mi
    n-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype
    -count 1024 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --g
    enotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-band
    s 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-ba
    nds 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq
    -bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf
    -gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable
    -optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --do-not-run-physical-phasing false --use-filtered-reads-for-annotations false --correct-overlapping-quality false --adaptive-pruning false --do-not-recover-dangling-branches false
    --recover-dangling-heads false --consensus false --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique
    -kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 1.0 --max-unpruned-variants 100 --debug-assemb
    ly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-g
    ap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-b
    ases false --min-base-quality-score 10 --smith-waterman JAVA --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --
    interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5
    false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output f
    alse --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default
    -annotations false --enable-all-annotations false",Version="4.1.1.0",Date="September 4, 2019 11:05:48 AM CEST">

    INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">

    INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">

    INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">

    INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">

    INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">

    INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">

    INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">

    INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">

    INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">

    INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">

    contig=<ID=NC_000913,length=4641652>

    source=HaplotypeCaller

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Autumn_2013_ALT_17 SAMPLE

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