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bahlolab / moimix

R package for inferring multiple infections from high-throughput sequencing data
http://bahlolab.github.io/moimix/
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problem with alleleCounts #33

Open jdaron opened 4 years ago

jdaron commented 4 years ago

Hi,

I have been using the very useful package moimix lately, but I was running into the issue below using alleleCounts, which could be helpful to report.

Here was the error message I got from alleleCounts:

counts <- alleleCounts(isolates) Error in dimnames(counts_matrix$alt) <- *vtmp* :

It turns out the problem was coming from my vcf file where the ID column of each variant wasn't specified ".". After updating my vcf file and specifying the ID for each variant everything went smoothly.

May be this error could be clarified in the alleleCounts function to avoid users to run into a similar issue.

Thanks for developing this wonderful package, Josquin

JacobAFW commented 2 years ago

Hi,

I am encountering the same error that @jdaron was getting above, and made the same change to my VCF file, but unfortunately this didn't work for me. I also get the error "Error in rowSums(x) : 'x' must be an array of at least two dimensions" when running 'getFws'. Not sure what is going on...

Here is a snapshot of my VCF, and below I have copied and pasted a bit more. Apologies for the text dump. Its a bit odd that github won't allow a VCF file format to be attached...

Please let me know if you need anything else, and any help would much appreciated.

vcf

fileformat=VCFv4.2

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FILTER= 1.0">

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GATKCommandLine.CombineGVCFs=<ID=CombineGVCFs,Version=3.8-1-0-gf15c1c3ef,Date="Tue Mar 01 11:39:48 GMT+10:00 2022",Epoch=1646098788851,CommandLineOptions="analysis_type=CombineGVCFs input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/g/data/pq84/malaria/data/ref_genomes/PKA1H1/fasta/strain_A1_H.1.Icor.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false 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source=PK_SB_DNA_054_DKDL210002183-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant157 source=PK_SB_DNA_055_DKDL210002184-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant158 source=PK_SB_DNA_056_DKDL210002185-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant159 source=PK_SB_DNA_057_DKDL210002186-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant160 source=PK_SB_DNA_058_DKDL210002187-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant161 source=PK_SB_DNA_059_DKDL210002188-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant162 source=PK_SB_DNA_060_DKDL210002189-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant163 source=PK_SB_DNA_061_DKDL210002190-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant164 source=PK_SB_DNA_062_DKDL210002191-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant165 source=PK_SB_DNA_063_DKDL210002192-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant166 source=PK_SB_DNA_064_DKDL210002193-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant167 source=PK_SB_DNA_065_DKDL210002194-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant168 source=PK_SB_DNA_066_DKDL210002195-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant169 source=PK_SB_DNA_067_DKDL210002196-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant170 source=PK_SB_DNA_068_DKDL210002197-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant171 source=PK_SB_DNA_069_DKDL210002198-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant172 source=PK_SB_DNA_070_DKDL210002199-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant173 source=PK_SB_DNA_071_DKDL210002200-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant174 source=PK_SB_DNA_072_DKDL210002201-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant175 source=PK_SB_DNA_073_DKDL210002202-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant176 source=PK_SB_DNA_074_DKDL210002203-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant177 source=PK_SB_DNA_075_DKDL210002204-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant178 source=PK_SB_DNA_076_DKDL210002205-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant179 source=PK_SB_DNA_077_DKDL210002206-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant180 source=PK_SB_DNA_078_DKDL210002207-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant181 source=PK_SB_DNA_079_DKDL210002208-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant182 source=PK_SB_DNA_080_DKDL210002209-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant183 source=PK_SB_DNA_081_DKDL210002210-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant184 source=PK_SB_DNA_082_DKDL210002211-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant185 source=PK_SB_DNA_083_DKDL210002212-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant186 source=PK_SB_DNA_084_DKDL210002213-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant187 source=PK_SB_DNA_085_DKDL210002214-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant188 source=PK_SB_DNA_086_DKDL210002215-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant189 source=PK_SB_DNA_087_DKDL210002216-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant190 source=PK_SB_DNA_088_DKDL210002217-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant191 source=PK_SB_DNA_089_DKDL210002218-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant192 source=PK_SB_DNA_090_DKDL210002219-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant193 source=PK_SB_DNA_091_DKDL210002220-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant194 source=PK_SB_DNA_092_DKDL210002221-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant195 source=PK_SB_DNA_093_DKDL210002222-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant196 source=PK_SB_DNA_094_DKDL210002223-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant197 source=SRR2221468.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant198 source=SRR2222335.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant199 source=SRR2225467.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant200 source=SRR2225571.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant201 source=SRR2225573.dupmarked.realigned.recal.g.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant202 source=SRR3135172.dupmarked.realigned.recal.g.vcf.gz)])] out=/g/data/pq84/malaria/Pk_clusters/outputs/04_Variant_calling/gatk/GATK_combined.g.vcf.gz convertToBasePairResolution=false breakBandsAtMultiplesOf=0 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,Version=3.8-1-0-gf15c1c3ef,Date="Tue Mar 01 15:25:13 GMT+10:00 2022",Epoch=1646112313094,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[/g/data/pq84/malaria/data/ref_genomes/PKA1H1/strain_A1_H.1.Icor.fasta.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/g/data/pq84/malaria/data/ref_genomes/PKA1H1/fasta/strain_A1_H.1.Icor.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=16 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=GATK_combined.g.vcf.gz)])] out=/g/data/pq84/malaria/Pk_clusters/outputs/04_Variant_calling/gatk/GATK_genotyped.vcf.gz includeNonVariantSites=false uniquifySamples=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=10.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 annotation=[] group=[StandardAnnotation] dbsnp=(RodBinding name= source=UNBOUND) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.8-1-0-gf15c1c3ef,Date="Fri Feb 25 16:15:28 GMT+10:00 2022",Epoch=1645769728112,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/g/data/pq84/malaria/Pk_clusters/outputs/03_Bam-pre/final_bam/SRR2225467.dupmarked.realigned.recal.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/g/data/pq84/malaria/data/ref_genomes/PKA1H1/fasta/strain_A1_H.1.Icor.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=3 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=200 errorCorrectKmers=false minPruning=3 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

GATKCommandLine.SelectVariants.2=<ID=SelectVariants,Version=3.8-1-0-gf15c1c3ef,Date="Tue May 10 11:17:38 GMT+10:00 2022",Epoch=1652145458076,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/g/data/pq84/malaria/Parasite_and_human_genetic_risk_factors_for_Pk_malaria/data/ref_genomes/PKA1H1/fasta/strain_A1_H.1.Icor.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=Consensus_fixed.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/g/data/pq84/malaria/Pk_Malaysian_Population_Genetics/outputs/04_Variant_calling/filtered/filter_tests/GVCFall_SNPs.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

GATKCommandLine.SelectVariants.3=<ID=SelectVariants,Version=3.8-1-0-gf15c1c3ef,Date="Tue May 10 12:10:52 GMT+10:00 2022",Epoch=1652148652740,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/g/data/pq84/malaria/Parasite_and_human_genetic_risk_factors_for_Pk_malaria/data/ref_genomes/PKA1H1/fasta/strain_A1_H.1.Icor.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/g/data/pq84/malaria/Pk_Malaysian_Population_Genetics/outputs/04_Variant_calling/filtered//FILTERED_SNPs.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/g/data/pq84/malaria/Pk_Malaysian_Population_Genetics/outputs/05_Analyses/PK_consensus_filtered_pass.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=true preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.8-1-0-gf15c1c3ef,Date="Tue Apr 19 10:43:20 GMT+10:00 2022",Epoch=1650329000220,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/g/data/pq84/malaria/Parasite_and_human_genetic_risk_factors_for_Pk_malaria/data/ref_genomes/PKA1H1/fasta/strain_A1_H.1.Icor.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=Consensus_with_duplicates_sorted.vcf.gz) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/g/data/pq84/malaria/Pk_Malaysian_Population_Genetics/outputs/04_Variant_calling/consensus/bcftools_version/Consensus.vcf.gz sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[2:] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

GATKCommandLine.VariantFiltration=<ID=VariantFiltration,Version=3.8-1-0-gf15c1c3ef,Date="Tue May 10 11:37:41 GMT+10:00 2022",Epoch=1652146661639,CommandLineOptions="analysis_type=VariantFiltration input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/g/data/pq84/malaria/Parasite_and_human_genetic_risk_factors_for_Pk_malaria/data/ref_genomes/PKA1H1/fasta/strain_A1_H.1.Icor.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/g/data/pq84/malaria/Pk_Malaysian_Population_Genetics/outputs/04_Variant_calling/filtered/filter_tests/GVCFall_SNPs.vcf) mask=(RodBinding name= source=UNBOUND) out=/g/data/pq84/malaria/Pk_Malaysian_Population_Genetics/outputs/04_Variant_calling/filtered/filter_tests/FILTERED_SNPs.vcf filterExpression=[QD < 15.0, FS > 1.0, MQ < 40.0] filterName=[QD15, FS1, MQ40] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false invertFilterExpression=false invertGenotypeFilterExpression=false setFilteredGtToNocall=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

GATKCommandLine=<ID=HaplotypeCaller,Version=3.2-2-gec30cee,Date="Wed Feb 09 23:40:36 ACST 2022",Epoch=1644415836190,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/home/jwestaway/pk_pipeline/Initial_Pk_subset/outputs/variant_calling/final_bams/PK_SB_DNA_080_DKDL210002209-1a_HWHGKDSXY_L4.dupmarked.realigned.recal.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/jwestaway/pk_pipeline/ref_genomes/PKA1H1/fasta/strain_A1_H.1.Icor.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bam_compression=null disable_bam_indexing=null generate_md5=null simplifyBAM=null bamWriterType=CALLED_HAPLOTYPES dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=3 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingTails=false consensus=false GVCFGQBands=[5, 20, 60] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 minPruning=3 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=200 mergeVariantsViaLD=false pair_hmm_implementation=VECTOR_LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debugGraphTransformations=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false noFpga=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 pcr_indel_model=CONSERVATIVE activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

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bcftoolsCommand=mpileup --threads 16 -f /g/data/pq84/malaria/data/ref_genomes/PKA1H1/fasta/strain_A1_H.1.Icor.fasta -b /g/data/pq84/malaria/Pk_clusters/outputs/03_Bam-pre/final_bam/input_bam_files.list -r ordered_PKNH_13_v2,ordered_PKNH_14_v2,PKNH_MIT_v2,new_API_strain_A1_H.1

bcftoolsVersion=1.12+htslib-1.12

bcftools_callCommand=call --threads 16 -m -Oz -a FORMAT/GQ,FORMAT/GP,INFO/PV4 -v -o /g/data/pq84/malaria/Pk_clusters/outputs/04_Variant_calling/bcftools/bcftools_genotyped_4.vcf.gz; Date=Wed Mar 16 16:35:25 2022

bcftools_callVersion=1.12+htslib-1.12

bcftools_mergeCommand=merge --threads 10 --force-samples -o /g/data/pq84/malaria/Pk_Malaysian_Population_Genetics/outputs/04_Variant_calling/consensus//merged_variants_only.vcf.gz /g/data/pq84/malaria/Pk_Malaysian_Population_Genetics/outputs/04_Variant_calling//gatk/GATK_genotyped.vcf.gz /g/data/pq84/malaria/Pk_Malaysian_Population_Genetics/outputs/04_Variant_calling//bcftools/bcftools_genotyped.vcf.gz; Date=Tue Apr 12 08:53:15 2022

bcftools_mergeVersion=1.12+htslib-1.12

bcftools_viewCommand=view /g/data/pq84/malaria/Pk_Malaysian_Population_Genetics/outputs/04_Variant_calling/consensus//merged_variants_only.vcf.gz; Date=Mon Apr 18 11:58:26 2022

bcftools_viewVersion=1.12+htslib-1.12

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reference=file:///g/data/pq84/malaria/Parasite_and_human_genetic_risk_factors_for_Pk_malaria/data/ref_genomes/PKA1H1/fasta/strain_A1_H.1.Icor.fasta

source=SelectVariants

bcftools_annotateVersion=1.12+htslib-1.12

bcftoolsannotateCommand=annotate --set-id +%CHROM_%POS_%REF\%FIRST_ALT PK_consensus_filtered_pass.vcf; Date=Wed May 11 16:01:59 2022

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ERR2214837 ERR2214838 ERR2214839 ERR2214840 ERR2214841 ERR2214842 ERR2214843 ERR2214844 ERR2214845 ERR2214846 ERR2214847 ERR2214848 ERR2214849 ERR2214850 ERR2214851 ERR2214852 ERR2214853 ERR2214854 ERR2214855 ERR2214856 ERR2214857 ERR274221 ERR274222 ERR274224 ERR274225 ERR3374031 ERR3374032 ERR3374033 ERR3374034 ERR3374035 ERR3374036 ERR3374037 ERR3374038 ERR3374039 ERR3374040 ERR3374041 ERR3374042 ERR3374043 ERR3374044 ERR3374045 ERR3374046 ERR3374047 ERR3374048 ERR3374049 ERR3374050 ERR3374051 ERR3374052 ERR3374053 ERR3374054 ERR3374055 ERR3374056 ERR3374057 ERR3374058 ERR366425 ERR366426 ERR985372 ERR985373 ERR985374 ERR985375 ERR985376 ERR985377 ERR985378 ERR985379 ERR985380 ERR985381 ERR985382 ERR985383 ERR985384 ERR985385 ERR985386 ERR985387 ERR985388 ERR985389 ERR985390 ERR985391 ERR985392 ERR985393 ERR985394 ERR985395 ERR985396 ERR985397 ERR985398 ERR985399 ERR985400 ERR985401 ERR985402 ERR985403 ERR985404 ERR985405 ERR985406 ERR985407 ERR985408 ERR985409 ERR985410 ERR985411 ERR985412 ERR985413 ERR985415 ERR985416 ERR985417 ERR985418 ERR985419 PK_SB_DNA_001_DKDL210002130-1a_HWHGKDSXY_L4 PK_SB_DNA_002_DKDL210002131-1a_HWHGKDSXY_L4 PK_SB_DNA_003_DKDL210002132-1a_HWHGKDSXY_L4 PK_SB_DNA_004_DKDL210002133-1a_HWHGKDSXY_L4 PK_SB_DNA_005_DKDL210002134-1a_HWHGKDSXY_L4 PK_SB_DNA_006_DKDL210002135-1a_HWHGKDSXY_L4 PK_SB_DNA_007_DKDL210002136-1a_HWHGKDSXY_L4 PK_SB_DNA_008_DKDL210002137-1a_HWHGKDSXY_L4 PK_SB_DNA_009_DKDL210002138-1a_HWHGKDSXY_L4 PK_SB_DNA_010_DKDL210002139-1a_HWHGKDSXY_L4 PK_SB_DNA_011_DKDL210002140-1a_HWHGKDSXY_L4 PK_SB_DNA_012_DKDL210002141-1a_HWHGKDSXY_L4 PK_SB_DNA_013_DKDL210002142-1a_HWHGKDSXY_L4 PK_SB_DNA_014_DKDL210002143-1a_HWHGKDSXY_L4 PK_SB_DNA_015_DKDL210002144-1a_HWHGKDSXY_L4 PK_SB_DNA_016_DKDL210002145-1a_HWHGKDSXY_L4 PK_SB_DNA_017_DKDL210002146-1a_HWHGKDSXY_L4 PK_SB_DNA_018_DKDL210002147-1a_HWHGKDSXY_L4 PK_SB_DNA_019_DKDL210002148-1a_HWHGKDSXY_L4 PK_SB_DNA_020_DKDL210002149-1a_HWHGKDSXY_L4 PK_SB_DNA_021_DKDL210002150-1a_HWHGKDSXY_L4 PK_SB_DNA_022_DKDL210002151-1a_HWHGKDSXY_L4 PK_SB_DNA_023_DKDL210002152-1a_HWHGKDSXY_L4 PK_SB_DNA_024_DKDL210002153-1a_HWHGKDSXY_L4 PK_SB_DNA_025_DKDL210002154-1a_HWHGKDSXY_L4 PK_SB_DNA_026_DKDL210002155-1a_HWHGKDSXY_L4 PK_SB_DNA_027_DKDL210002156-1a_HWHGKDSXY_L4 PK_SB_DNA_028_DKDL210002157-1a_HWHGKDSXY_L4 PK_SB_DNA_029_DKDL210002158-1a_HWHGKDSXY_L4 PK_SB_DNA_030_DKDL210002159-1a_HWHGKDSXY_L4 PK_SB_DNA_031_DKDL210002160-1a_HWHGKDSXY_L4 PK_SB_DNA_032_DKDL210002161-1a_HWHGKDSXY_L4 PK_SB_DNA_033_DKDL210002162-1a_HWHGKDSXY_L4 PK_SB_DNA_034_DKDL210002163-1a_HWHGKDSXY_L4 PK_SB_DNA_035_DKDL210002164-1a_HWHGKDSXY_L4 PK_SB_DNA_036_DKDL210002165-1a_HWHGKDSXY_L4 PK_SB_DNA_037_DKDL210002166-1a_HWHGKDSXY_L4 PK_SB_DNA_038_DKDL210002167-1a_HWHGKDSXY_L4 PK_SB_DNA_039_DKDL210002168-1a_HWHGKDSXY_L4 PK_SB_DNA_040_DKDL210002169-1a_HWHGKDSXY_L4 PK_SB_DNA_041_DKDL210002170-1a_HWHGKDSXY_L4 PK_SB_DNA_042_DKDL210002171-1a_HWHGKDSXY_L4 PK_SB_DNA_043_DKDL210002172-1a_HWHGKDSXY_L4 PK_SB_DNA_044_DKDL210002173-1a_HWHGKDSXY_L4 PK_SB_DNA_045_DKDL210002174-1a_HWHGKDSXY_L4 PK_SB_DNA_046_DKDL210002175-1a_HWHGKDSXY_L4 PK_SB_DNA_047_DKDL210002176-1a_HWHGKDSXY_L4 PK_SB_DNA_048_DKDL210002177-1a_HWHGKDSXY_L4 PK_SB_DNA_049_DKDL210002178-1a_HWHGKDSXY_L4 PK_SB_DNA_050_DKDL210002179-1a_HWHGKDSXY_L4 PK_SB_DNA_051_DKDL210002180-1a_HWHGKDSXY_L4 PK_SB_DNA_052_DKDL210002181-1a_HWHGKDSXY_L4 PK_SB_DNA_053_DKDL210002182-1a_HWHGKDSXY_L4 PK_SB_DNA_054_DKDL210002183-1a_HWHGKDSXY_L4 PK_SB_DNA_055_DKDL210002184-1a_HWHGKDSXY_L4 PK_SB_DNA_056_DKDL210002185-1a_HWHGKDSXY_L4 PK_SB_DNA_057_DKDL210002186-1a_HWHGKDSXY_L4 PK_SB_DNA_058_DKDL210002187-1a_HWHGKDSXY_L4 PK_SB_DNA_059_DKDL210002188-1a_HWHGKDSXY_L4 PK_SB_DNA_060_DKDL210002189-1a_HWHGKDSXY_L4 PK_SB_DNA_061_DKDL210002190-1a_HWHGKDSXY_L4 PK_SB_DNA_062_DKDL210002191-1a_HWHGKDSXY_L4 PK_SB_DNA_063_DKDL210002192-1a_HWHGKDSXY_L4 PK_SB_DNA_064_DKDL210002193-1a_HWHGKDSXY_L4 PK_SB_DNA_065_DKDL210002194-1a_HWHGKDSXY_L4 PK_SB_DNA_066_DKDL210002195-1a_HWHGKDSXY_L4 PK_SB_DNA_067_DKDL210002196-1a_HWHGKDSXY_L4 PK_SB_DNA_068_DKDL210002197-1a_HWHGKDSXY_L4 PK_SB_DNA_069_DKDL210002198-1a_HWHGKDSXY_L4 PK_SB_DNA_070_DKDL210002199-1a_HWHGKDSXY_L4 PK_SB_DNA_071_DKDL210002200-1a_HWHGKDSXY_L4 PK_SB_DNA_072_DKDL210002201-1a_HWHGKDSXY_L4 PK_SB_DNA_073_DKDL210002202-1a_HWHGKDSXY_L4 PK_SB_DNA_074_DKDL210002203-1a_HWHGKDSXY_L4 PK_SB_DNA_075_DKDL210002204-1a_HWHGKDSXY_L4 PK_SB_DNA_076_DKDL210002205-1a_HWHGKDSXY_L4 PK_SB_DNA_077_DKDL210002206-1a_HWHGKDSXY_L4 PK_SB_DNA_078_DKDL210002207-1a_HWHGKDSXY_L4 PK_SB_DNA_079_DKDL210002208-1a_HWHGKDSXY_L4 PK_SB_DNA_080_DKDL210002209-1a_HWHGKDSXY_L4 PK_SB_DNA_081_DKDL210002210-1a_HWHGKDSXY_L4 PK_SB_DNA_082_DKDL210002211-1a_HWHGKDSXY_L4 PK_SB_DNA_083_DKDL210002212-1a_HWHGKDSXY_L4 PK_SB_DNA_084_DKDL210002213-1a_HWHGKDSXY_L4 PK_SB_DNA_085_DKDL210002214-1a_HWHGKDSXY_L4 PK_SB_DNA_086_DKDL210002215-1a_HWHGKDSXY_L4 PK_SB_DNA_087_DKDL210002216-1a_HWHGKDSXY_L4 PK_SB_DNA_088_DKDL210002217-1a_HWHGKDSXY_L4 PK_SB_DNA_089_DKDL210002218-1a_HWHGKDSXY_L4 PK_SB_DNA_090_DKDL210002219-1a_HWHGKDSXY_L4 PK_SB_DNA_091_DKDL210002220-1a_HWHGKDSXY_L4 PK_SB_DNA_092_DKDL210002221-1a_HWHGKDSXY_L4 PK_SB_DNA_093_DKDL210002222-1a_HWHGKDSXY_L4 PK_SB_DNA_094_DKDL210002223-1a_HWHGKDSXY_L4 SRR2221468 SRR2222335 SRR2225467 SRR2225571 SRR2225573 SRR3135172

ordered_PKNH_01_v2 574 ordered_PKNH_01_v2_574_C_A C A 2714.69 PASS AC=2;AF=0.038;AN=52;BQB=1.16842e-19;DP=605;DP4=378,287,405,204;ExcessHet=0.0755;FS=0;InbreedingCoeff=0.032;MQ=50.14;MQ0=0;MQ0F=0.178903;MQB=3.08374e-06;MQSB=0.0257201;PV4=0.000437527,1,1,1;QD=15.09;RPB=4.11692e-05;SGB=148.232;SOR=1.863;VDB=1 GT:AD:DP:GQ:PL ./.:0,0:0:.:0,0,0 0/0:1,0:1:3:0,3,13 ./.:0,0:0:.:0,0,0 ./.:2,0:2:.:0,0,0 ./.:1,0:1:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:1,0:1:.:0,0,0 ./.:1,0:1:.:0,0,0 ./.:1,0:1:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:1,0:1:.:0,0,0 ./.:1,0:1:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:1,0:1:.:0,0,0 ./.:1,0:1:.:0,0,0 ./.:1,0:1:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:6,0:6:.:0,0,0 0/0:1,0:1:3:0,3,26 ./.:1,0:1:.:0,0,0 ./.:7,0:7:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 0/0:1,0:1:3:0,3,12 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:2,0:2:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 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./.:12,0:12:.:0,0,0 ./.:4,0:4:.:0,0,0 ./.:10,0:10:.:0,0,0 ./.:31,0:31:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:5,0:5:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:2,0:2:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:10,0:10:.:0,0,0 ./.:12,0:12:.:0,0,0 ./.:11,0:11:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:4,0:4:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 1/1:0,8:8:22:162,22,0 ./.:0,0:0:.:0,0,0 ./.:1,0:1:.:0,0,0 ./.:3,0:3:.:0,0,0 ./.:4,0:4:.:0,0,0 0/0:2,0:2:6:0,6,41 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:2,0:2:.:0,0,0 ./.:3,0:3:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:5,0:5:.:0,0,0 ./.:6,0:6:.:0,0,0 ./.:10,0:10:.:0,0,0 ./.:8,0:8:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:36,0:36:.:0,0,0 ./.:1,0:1:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:1,0:1:.:0,0,0 ./.:1,0:1:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:3,0:3:.:0,0,0 ./.:3,0:3:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:14,0:14:.:0,0,0 ordered_PKNH_01_v2 3538 ordered_PKNH_01_v2_3538_A_G A G 312.48 PASS AC=2;AF=0.018;AN=112;BQB=0.410667;BaseQRankSum=-0.312;ClippingRankSum=2.28;DP=397;DP4=1028,753,90,41;ExcessHet=3.4851;FS=0;InbreedingCoeff=-0.1622;MQ=40.35;MQ0=0;MQ0F=0.345779;MQB=0.0150212;MQRankSum=0.727;MQSB=2.37954e-06;PV4=0.0166283,1,1,1;QD=18.38;RPB=0.244136;ReadPosRankSum=1.49;SGB=-300.125;SOR=0.813;VDB=0.423162 GT:AD:DP:GQ:PL ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:1,0:1:.:0,0,0 0/0:3,0:3:0:0,0,21 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 0/0:2,0:2:3:0,3,45 0/0:2,0:2:6:0,6,38 ./.:0,0:0:.:0,0,0 ./.:1,0:1:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 0/0:11,0:11:0:0,0,170 0/0:3,0:3:9:0,9,73 ./.:0,0:0:.:0,0,0 0/0:4,0:4:3:0,3,45 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:2,0:2:.:0,0,0 0/0:2,0:2:6:0,6,34 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