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Commit 317e9316 authored by van den Berg's avatar van den Berg
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Add initial pytest-workflow tests and data

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2 merge requests!2Add testing to vcf-to-varda,!1Gitlab ci
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test/data/16699289_chrM.g.vcf 0 → 100644
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##fileformat=VCFv4.2
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and 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=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.7-0-gcfedb67,Date="Fri Mar 13 15:58:36 UTC 2020",Epoch=1584115116921,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[16699289/bams/16699289.markdup.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[chrM:1-16571] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/exports/capture-lumc/dependencies/reference_files/gatk_bundle_hg19/ucsc.hg19_nohap.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=16699289/bams/16699289.baserecal.grp 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 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=dbsnp source=/exports/capture-lumc/dependencies/reference_files/gatk_bundle_hg19/dbsnp_137.hg19_nohap.noclin.vcf.gz) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[StandardAnnotation, StandardHCAnnotation] 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=6 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=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 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">
##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)
##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)
##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)
##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive)
##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive)
##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive)
##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive)
##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive)
##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive)
##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive)
##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive)
##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive)
##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive)
##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive)
##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive)
##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive)
##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive)
##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive)
##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive)
##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive)
##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive)
##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive)
##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive)
##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive)
##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive)
##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive)
##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive)
##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive)
##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive)
##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive)
##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive)
##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive)
##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive)
##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive)
##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive)
##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive)
##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive)
##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive)
##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive)
##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive)
##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive)
##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive)
##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive)
##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive)
##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive)
##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive)
##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive)
##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive)
##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive)
##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive)
##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive)
##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive)
##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive)
##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive)
##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive)
##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive)
##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive)
##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive)
##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive)
##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive)
##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive)
##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive)
##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive)
##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive)
##GVCFBlock99-100=minGQ=99(inclusive),maxGQ=100(exclusive)
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##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=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##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=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##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_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##contig=<ID=chrM,length=16571,assembly=hg19>
##contig=<ID=chr1,length=249250621,assembly=hg19>
##contig=<ID=chr2,length=243199373,assembly=hg19>
##contig=<ID=chr3,length=198022430,assembly=hg19>
##contig=<ID=chr4,length=191154276,assembly=hg19>
##contig=<ID=chr5,length=180915260,assembly=hg19>
##contig=<ID=chr6,length=171115067,assembly=hg19>
##contig=<ID=chr7,length=159138663,assembly=hg19>
##contig=<ID=chr8,length=146364022,assembly=hg19>
##contig=<ID=chr9,length=141213431,assembly=hg19>
##contig=<ID=chr10,length=135534747,assembly=hg19>
##contig=<ID=chr11,length=135006516,assembly=hg19>
##contig=<ID=chr12,length=133851895,assembly=hg19>
##contig=<ID=chr13,length=115169878,assembly=hg19>
##contig=<ID=chr14,length=107349540,assembly=hg19>
##contig=<ID=chr15,length=102531392,assembly=hg19>
##contig=<ID=chr16,length=90354753,assembly=hg19>
##contig=<ID=chr17,length=81195210,assembly=hg19>
##contig=<ID=chr18,length=78077248,assembly=hg19>
##contig=<ID=chr19,length=59128983,assembly=hg19>
##contig=<ID=chr20,length=63025520,assembly=hg19>
##contig=<ID=chr21,length=48129895,assembly=hg19>
##contig=<ID=chr22,length=51304566,assembly=hg19>
##contig=<ID=chrX,length=155270560,assembly=hg19>
##contig=<ID=chrY,length=59373566,assembly=hg19>
##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19>
##contig=<ID=chr1_gl000192_random,length=547496,assembly=hg19>
##contig=<ID=chr4_gl000193_random,length=189789,assembly=hg19>
##contig=<ID=chr4_gl000194_random,length=191469,assembly=hg19>
##contig=<ID=chr7_gl000195_random,length=182896,assembly=hg19>
##contig=<ID=chr8_gl000196_random,length=38914,assembly=hg19>
##contig=<ID=chr8_gl000197_random,length=37175,assembly=hg19>
##contig=<ID=chr9_gl000198_random,length=90085,assembly=hg19>
##contig=<ID=chr9_gl000199_random,length=169874,assembly=hg19>
##contig=<ID=chr9_gl000200_random,length=187035,assembly=hg19>
##contig=<ID=chr9_gl000201_random,length=36148,assembly=hg19>
##contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19>
##contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19>
##contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19>
##contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19>
##contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19>
##contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19>
##contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19>
##contig=<ID=chr19_gl000209_random,length=159169,assembly=hg19>
##contig=<ID=chr21_gl000210_random,length=27682,assembly=hg19>
##contig=<ID=chrUn_gl000211,length=166566,assembly=hg19>
##contig=<ID=chrUn_gl000212,length=186858,assembly=hg19>
##contig=<ID=chrUn_gl000213,length=164239,assembly=hg19>
##contig=<ID=chrUn_gl000214,length=137718,assembly=hg19>
##contig=<ID=chrUn_gl000215,length=172545,assembly=hg19>
##contig=<ID=chrUn_gl000216,length=172294,assembly=hg19>
##contig=<ID=chrUn_gl000217,length=172149,assembly=hg19>
##contig=<ID=chrUn_gl000218,length=161147,assembly=hg19>
##contig=<ID=chrUn_gl000219,length=179198,assembly=hg19>
##contig=<ID=chrUn_gl000220,length=161802,assembly=hg19>
##contig=<ID=chrUn_gl000221,length=155397,assembly=hg19>
##contig=<ID=chrUn_gl000222,length=186861,assembly=hg19>
##contig=<ID=chrUn_gl000223,length=180455,assembly=hg19>
##contig=<ID=chrUn_gl000224,length=179693,assembly=hg19>
##contig=<ID=chrUn_gl000225,length=211173,assembly=hg19>
##contig=<ID=chrUn_gl000226,length=15008,assembly=hg19>
##contig=<ID=chrUn_gl000227,length=128374,assembly=hg19>
##contig=<ID=chrUn_gl000228,length=129120,assembly=hg19>
##contig=<ID=chrUn_gl000229,length=19913,assembly=hg19>
##contig=<ID=chrUn_gl000230,length=43691,assembly=hg19>
##contig=<ID=chrUn_gl000231,length=27386,assembly=hg19>
##contig=<ID=chrUn_gl000232,length=40652,assembly=hg19>
##contig=<ID=chrUn_gl000233,length=45941,assembly=hg19>
##contig=<ID=chrUn_gl000234,length=40531,assembly=hg19>
##contig=<ID=chrUn_gl000235,length=34474,assembly=hg19>
##contig=<ID=chrUn_gl000236,length=41934,assembly=hg19>
##contig=<ID=chrUn_gl000237,length=45867,assembly=hg19>
##contig=<ID=chrUn_gl000238,length=39939,assembly=hg19>
##contig=<ID=chrUn_gl000239,length=33824,assembly=hg19>
##contig=<ID=chrUn_gl000240,length=41933,assembly=hg19>
##contig=<ID=chrUn_gl000241,length=42152,assembly=hg19>
##contig=<ID=chrUn_gl000242,length=43523,assembly=hg19>
##contig=<ID=chrUn_gl000243,length=43341,assembly=hg19>
##contig=<ID=chrUn_gl000244,length=39929,assembly=hg19>
##contig=<ID=chrUn_gl000245,length=36651,assembly=hg19>
##contig=<ID=chrUn_gl000246,length=38154,assembly=hg19>
##contig=<ID=chrUn_gl000247,length=36422,assembly=hg19>
##contig=<ID=chrUn_gl000248,length=39786,assembly=hg19>
##contig=<ID=chrUn_gl000249,length=38502,assembly=hg19>
##reference=file:///exports/capture-lumc/dependencies/reference_files/gatk_bundle_hg19/ucsc.hg19_nohap.fasta
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 16699289
chrM 1 . G <NON_REF> . . END=72 GT:DP:GQ:MIN_DP:PL 0/0:96:99:54:0,120,1800
chrM 73 . G A,<NON_REF> 4062.77 . DP=131;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=444604.00 GT:AD:DP:GQ:PL:SB 1/1:0,126,0:126:99:4091,378,0,4091,378,4091:0,0,66,60
chrM 74 . T <NON_REF> . . END=149 GT:DP:GQ:MIN_DP:PL 0/0:136:99:123:0,120,1800
chrM 150 . T C,<NON_REF> 5149.77 . DP=130;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=468000.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,117,0:117:99:0|1:150_T_C:5178,352,0,5178,352,5178:0,0,58,59
chrM 151 . C <NON_REF> . . END=151 GT:DP:GQ:MIN_DP:PL 0/0:122:99:122:0,120,1800
chrM 152 rs117135796 T C,<NON_REF> 5149.77 . DB;DP=126;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=453600.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,113,0:113:99:0|1:150_T_C:5178,352,0,5178,352,5178:0,0,57,56
chrM 153 . A <NON_REF> . . END=194 GT:DP:GQ:MIN_DP:PL 0/0:101:99:93:0,120,1800
chrM 195 . C T,<NON_REF> 2959.77 . DP=98;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=352800.00 GT:AD:DP:GQ:PL:SB 1/1:0,82,0:82:99:2988,246,0,2988,246,2988:0,0,36,46
chrM 196 . T <NON_REF> . . END=301 GT:DP:GQ:MIN_DP:PL 0/0:80:99:47:0,114,1401
chrM 302 . A <NON_REF> . . END=303 GT:DP:GQ:MIN_DP:PL 0/0:50:85:49:0,85,1355
chrM 304 . C <NON_REF> . . END=310 GT:DP:GQ:MIN_DP:PL 0/0:53:99:51:0,108,1620
chrM 311 . T <NON_REF> . . END=311 GT:DP:GQ:MIN_DP:PL 0/0:42:97:42:0,97,1515
chrM 312 . C <NON_REF> . . END=409 GT:DP:GQ:MIN_DP:PL 0/0:75:99:47:0,103,1765
chrM 410 . A T,<NON_REF> 3234.77 . DP=101;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=361330.00 GT:AD:DP:GQ:PL:SB 1/1:0,99,0:99:99:3263,296,0,3263,296,3263:0,0,43,56
chrM 411 . G <NON_REF> . . END=2260 GT:DP:GQ:MIN_DP:PL 0/0:117:99:57:0,120,1800
chrM 2261 . C T,<NON_REF> 2900.77 . DP=97;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=349200.00 GT:AD:DP:GQ:PL:SB 1/1:0,93,0:93:99:2929,276,0,2929,276,2929:0,0,52,41
chrM 2262 . A <NON_REF> . . END=2353 GT:DP:GQ:MIN_DP:PL 0/0:105:99:88:0,120,1800
chrM 2354 . C T,<NON_REF> 3755.77 . DP=117;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=421200.00 GT:AD:DP:GQ:PL:SB 1/1:0,114,0:114:99:3784,341,0,3784,341,3784:0,0,66,48
chrM 2355 . A <NON_REF> . . END=2484 GT:DP:GQ:MIN_DP:PL 0/0:117:99:104:0,120,1800
chrM 2485 . C T,<NON_REF> 4129.77 . DP=121;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=435600.00 GT:AD:DP:GQ:PL:SB 1/1:0,121,0:121:99:4158,362,0,4158,362,4158:0,0,68,53
chrM 2486 . C <NON_REF> . . END=2707 GT:DP:GQ:MIN_DP:PL 0/0:143:99:116:0,120,1800
chrM 2708 . G A,<NON_REF> 4474.77 . DP=127;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=454834.00 GT:AD:DP:GQ:PL:SB 1/1:0,127,0:127:99:4503,381,0,4503,381,4503:0,0,61,66
chrM 2709 . A <NON_REF> . . END=3578 GT:DP:GQ:MIN_DP:PL 0/0:120:99:82:0,120,1800
chrM 3579 . T <NON_REF> . . END=3579 GT:DP:GQ:MIN_DP:PL 0/0:104:0:104:0,0,2184
chrM 3580 . A <NON_REF> . . END=3590 GT:DP:GQ:MIN_DP:PL 0/0:140:99:130:0,120,1800
chrM 3591 . T <NON_REF> . . END=3591 GT:DP:GQ:MIN_DP:PL 0/0:97:84:97:0,84,2695
chrM 3592 . G <NON_REF> . . END=4745 GT:DP:GQ:MIN_DP:PL 0/0:109:99:57:0,120,1800
chrM 4746 . A G,<NON_REF> 2693.77 . DP=82;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=172445.00 GT:AD:DP:GQ:PL:SB 1/1:0,81,0:81:99:2722,242,0,2722,242,2722:0,0,40,41
chrM 4747 . T <NON_REF> . . END=5580 GT:DP:GQ:MIN_DP:PL 0/0:123:99:74:0,120,1800
chrM 5581 . C T,<NON_REF> 3091.77 . DP=96;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=213064.00 GT:AD:DP:GQ:PL:SB 1/1:0,95,0:95:99:3120,285,0,3120,285,3120:0,0,53,42
chrM 5582 . A <NON_REF> . . END=7028 GT:DP:GQ:MIN_DP:PL 0/0:144:99:64:0,104,1800
chrM 7029 . T C,<NON_REF> 3034.77 . DP=94;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=161816.00 GT:AD:DP:GQ:PL:SB 1/1:0,94,0:94:99:3063,282,0,3063,282,3063:0,0,47,47
chrM 7030 . C <NON_REF> . . END=7337 GT:DP:GQ:MIN_DP:PL 0/0:123:99:81:0,120,1800
chrM 7338 . G A,<NON_REF> 3647.77 . DP=111;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=282778.00 GT:AD:DP:GQ:PL:SB 1/1:0,111,0:111:99:3676,333,0,3676,333,3676:0,0,51,60
chrM 7339 . A <NON_REF> . . END=8701 GT:DP:GQ:MIN_DP:PL 0/0:150:99:83:0,120,1800
chrM 8702 . G A,<NON_REF> 55738.77 . BaseQRankSum=-2.533;ClippingRankSum=0.000;DP=1455;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=-0.857;RAW_MQ=4888503.00;ReadPosRankSum=-1.220 GT:AD:DP:GQ:PL:SB 1/1:3,1444,0:1447:99:55767,4213,0,55776,4330,55893:3,0,1352,92
chrM 8703 . C <NON_REF> . . END=9377 GT:DP:GQ:MIN_DP:PL 0/0:1504:99:438:0,120,1800
chrM 9378 . G A,<NON_REF> 15302.77 . BaseQRankSum=1.903;ClippingRankSum=0.000;DP=430;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=-1.678;RAW_MQ=1088513.00;ReadPosRankSum=-0.842 GT:AD:DP:GQ:PL:SB 1/1:2,425,0:427:99:15331,1231,0,15337,1275,15380:1,1,114,311
chrM 9379 . T <NON_REF> . . END=9540 GT:DP:GQ:MIN_DP:PL 0/0:319:99:256:0,120,1800
chrM 9541 . C T,<NON_REF> 7951.77 . BaseQRankSum=-1.006;ClippingRankSum=0.000;DP=242;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.000;RAW_MQ=869449.00;ReadPosRankSum=1.484 GT:AD:DP:GQ:PL:SB 1/1:1,238,0:239:99:7980,670,0,7983,708,8021:0,1,68,170
chrM 9542 . T <NON_REF> . . END=10398 GT:DP:GQ:MIN_DP:PL 0/0:121:99:81:0,120,1800
chrM 10399 . G A,<NON_REF> 2937.77 . DP=93;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=334800.00 GT:AD:DP:GQ:PL:SB 1/1:0,92,0:92:99:2966,275,0,2966,275,2966:0,0,51,41
chrM 10400 . C <NON_REF> . . END=10819 GT:DP:GQ:MIN_DP:PL 0/0:120:99:80:0,120,1800
chrM 10820 . G A,<NON_REF> 3446.77 . DP=114;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=401514.00 GT:AD:DP:GQ:PL:SB 1/1:0,111,0:111:99:3475,331,0,3475,331,3475:0,0,63,48
chrM 10821 . C <NON_REF> . . END=10873 GT:DP:GQ:MIN_DP:PL 0/0:110:99:99:0,120,1800
chrM 10874 . C T,<NON_REF> 3100.77 . DP=100;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=357320.00 GT:AD:DP:GQ:PL:SB 1/1:0,98,0:98:99:3129,292,0,3129,292,3129:0,0,48,50
chrM 10875 . C <NON_REF> . . END=11017 GT:DP:GQ:MIN_DP:PL 0/0:93:99:78:0,120,1800
chrM 11018 . C T,<NON_REF> 2952.77 . DP=90;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=316771.00 GT:AD:DP:GQ:PL:SB 1/1:0,89,0:89:99:2981,265,0,2981,265,2981:0,0,45,44
chrM 11019 . G <NON_REF> . . END=11719 GT:DP:GQ:MIN_DP:PL 0/0:142:99:91:0,120,1800
chrM 11720 . A G,<NON_REF> 5996.77 . DP=133;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=442009.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,133,0:133:99:0|1:11720_A_G:6025,412,0,6025,412,6025:0,0,68,65
chrM 11721 . C <NON_REF> . . END=11722 GT:DP:GQ:MIN_DP:PL 0/0:135:99:134:0,120,1800
chrM 11723 . C T,<NON_REF> 5947.77 . DP=132;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=438409.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,132,0:132:99:0|1:11720_A_G:5976,406,0,5976,406,5976:0,0,66,66
chrM 11724 . A <NON_REF> . . END=12705 GT:DP:GQ:MIN_DP:PL 0/0:111:99:73:0,120,1800
chrM 12706 . T C,<NON_REF> 3690.77 . DP=124;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=446400.00 GT:AD:DP:GQ:PL:SB 1/1:0,115,0:115:99:3719,343,0,3719,343,3719:0,0,62,53
chrM 12707 . T <NON_REF> . . END=12850 GT:DP:GQ:MIN_DP:PL 0/0:126:99:118:0,120,1800
chrM 12851 . G A,<NON_REF> 3972.77 . DP=128;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=460800.00 GT:AD:DP:GQ:PL:SB 1/1:0,128,0:128:99:4001,380,0,4001,380,4001:0,0,74,54
chrM 12852 . T <NON_REF> . . END=13326 GT:DP:GQ:MIN_DP:PL 0/0:148:99:120:0,120,1800
chrM 13327 . T C,<NON_REF> 5000.77 . DP=150;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=535069.00 GT:AD:DP:GQ:PL:SB 1/1:0,148,0:148:99:5029,445,0,5029,445,5029:0,0,66,82
chrM 13328 . A <NON_REF> . . END=13680 GT:DP:GQ:MIN_DP:PL 0/0:121:99:104:0,120,1800
chrM 13681 . C T,<NON_REF> 3752.77 . DP=123;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=442800.00 GT:AD:DP:GQ:PL:SB 1/1:0,121,0:121:99:3781,361,0,3781,361,3781:0,0,67,54
chrM 13682 . A <NON_REF> . . END=14212 GT:DP:GQ:MIN_DP:PL 0/0:100:99:75:0,120,1800
chrM 14213 . C T,<NON_REF> 2504.77 . DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=288097.00 GT:AD:DP:GQ:PL:SB 1/1:0,77,0:77:99:2533,231,0,2533,231,2533:0,0,39,38
chrM 14214 . A <NON_REF> . . END=14580 GT:DP:GQ:MIN_DP:PL 0/0:126:99:81:0,120,1800
chrM 14581 . G A,<NON_REF> 2819.77 . DP=90;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=323649.00 GT:AD:DP:GQ:PL:SB 1/1:0,88,0:88:99:2848,262,0,2848,262,2848:0,0,43,45
chrM 14582 . T <NON_REF> . . END=14766 GT:DP:GQ:MIN_DP:PL 0/0:77:99:66:0,120,1800
chrM 14767 . T C,<NON_REF> 2914.77 . DP=93;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=326448.00 GT:AD:DP:GQ:PL:SB 1/1:0,88,0:88:99:2943,264,0,2943,264,2943:0,0,54,34
chrM 14768 . T <NON_REF> . . END=14831 GT:DP:GQ:MIN_DP:PL 0/0:94:99:87:0,120,1800
chrM 14832 . G A,<NON_REF> 3447.77 . DP=111;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=397296.00 GT:AD:DP:GQ:PL:SB 1/1:0,108,0:108:99:3476,323,0,3476,323,3476:0,0,63,45
chrM 14833 . C <NON_REF> . . END=14872 GT:DP:GQ:MIN_DP:PL 0/0:119:99:113:0,120,1800
chrM 14873 . C T,<NON_REF> 3719.77 . DP=120;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=432000.00 GT:AD:DP:GQ:PL:SB 1/1:0,120,0:120:99:3748,358,0,3748,358,3748:0,0,64,56
chrM 14874 . C <NON_REF> . . END=14905 GT:DP:GQ:MIN_DP:PL 0/0:127:99:118:0,120,1800
chrM 14906 . A G,<NON_REF> 4327.77 . DP=127;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=452900.00 GT:AD:DP:GQ:PL:SB 1/1:0,127,0:127:99:4356,381,0,4356,381,4356:0,0,71,56
chrM 14907 . C <NON_REF> . . END=15301 GT:DP:GQ:MIN_DP:PL 0/0:113:99:90:0,120,1800
chrM 15302 . A G,<NON_REF> 3502.77 . DP=105;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=378000.00 GT:AD:DP:GQ:PL:SB 1/1:0,102,0:102:99:3531,306,0,3531,306,3531:0,0,48,54
chrM 15303 . C <NON_REF> . . END=15932 GT:DP:GQ:MIN_DP:PL 0/0:103:99:84:0,120,1800
chrM 15933 . C T,<NON_REF> 3115.77 . DP=97;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=349200.00 GT:AD:DP:GQ:PL:SB 1/1:0,94,0:94:99:3144,282,0,3144,282,3144:0,0,47,47
chrM 15934 . G <NON_REF> . . END=16023 GT:DP:GQ:MIN_DP:PL 0/0:100:99:94:0,120,1800
chrM 16024 . G A,<NON_REF> 1312.77 . BaseQRankSum=-2.823;ClippingRankSum=0.000;DP=111;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=399600.00;ReadPosRankSum=0.794 GT:AD:DP:GQ:PL:SB 0/1:55,53,0:108:99:1341,0,1621,1506,1779,3285:32,23,23,30
chrM 16025 . T <NON_REF> . . END=16161 GT:DP:GQ:MIN_DP:PL 0/0:100:99:92:0,102,1530
chrM 16162 . T <NON_REF> . . END=16162 GT:DP:GQ:MIN_DP:PL 0/0:109:87:109:0,87,1305
chrM 16163 . A <NON_REF> . . END=16165 GT:DP:GQ:MIN_DP:PL 0/0:111:75:111:0,75,1125
chrM 16166 . A <NON_REF> . . END=16167 GT:DP:GQ:MIN_DP:PL 0/0:111:69:111:0,69,1035
chrM 16168 . C <NON_REF> . . END=16169 GT:DP:GQ:MIN_DP:PL 0/0:112:51:111:0,51,765
chrM 16170 . C <NON_REF> . . END=16170 GT:DP:GQ:MIN_DP:PL 0/0:114:45:114:0,45,675
chrM 16171 . A <NON_REF> . . END=16172 GT:DP:GQ:MIN_DP:PL 0/0:115:42:114:0,42,630
chrM 16173 . C T,<NON_REF> 5037.77 . DP=116;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=415798.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,109,0:109:99:0|1:16173_C_T:5066,343,0,5066,343,5066:0,0,54,55
chrM 16174 . C <NON_REF> . . END=16174 GT:DP:GQ:MIN_DP:PL 0/0:119:42:119:0,42,630
chrM 16175 . C <NON_REF> . . END=16175 GT:DP:GQ:MIN_DP:PL 0/0:120:33:120:0,33,495
chrM 16176 . A <NON_REF> . . END=16178 GT:DP:GQ:MIN_DP:PL 0/0:119:27:114:0,27,405
chrM 16179 . T <NON_REF> . . END=16179 GT:DP:GQ:MIN_DP:PL 0/0:116:24:116:0,24,360
chrM 16180 . C <NON_REF> . . END=16180 GT:DP:GQ:MIN_DP:PL 0/0:119:15:119:0,15,225
chrM 16181 . A <NON_REF> . . END=16182 GT:DP:GQ:MIN_DP:PL 0/0:119:3:119:0,3,45
chrM 16183 . AC A,<NON_REF> 5020.73 . DP=120;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=430198.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,113,0:113:99:0|1:16173_C_T:5058,340,0,5058,340,5058:0,0,56,57
chrM 16185 . C A,<NON_REF> 5029.77 . DP=119;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=426598.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,112,0:112:99:0|1:16173_C_T:5058,340,0,5058,340,5058:0,0,56,56
chrM 16186 . C <NON_REF> . . END=16190 GT:DP:GQ:MIN_DP:PL 0/0:113:99:112:0,120,1800
chrM 16191 . C T,<NON_REF> 4831.77 . DP=115;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=412198.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,108,0:108:99:0|1:16173_C_T:4860,328,0,4860,328,4860:0,0,56,52
chrM 16192 . C <NON_REF> . . END=16224 GT:DP:GQ:MIN_DP:PL 0/0:116:99:110:0,120,1800
chrM 16225 . T C,<NON_REF> 3434.77 . DP=117;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=419398.00 GT:AD:DP:GQ:PL:SB 1/1:0,110,0:110:99:3463,329,0,3463,329,3463:0,0,58,52
chrM 16226 . T <NON_REF> . . END=16321 GT:DP:GQ:MIN_DP:PL 0/0:117:99:107:0,120,1800
chrM 16322 . T C,<NON_REF> 3589.77 . DP=118;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=424800.00 GT:AD:DP:GQ:PL:SB 1/1:0,114,0:114:99:3618,340,0,3618,340,3618:0,0,56,58
chrM 16323 . C <NON_REF> . . END=16520 GT:DP:GQ:MIN_DP:PL 0/0:126:99:107:0,120,1800
chrM 16521 . C T,<NON_REF> 4251.77 . BaseQRankSum=1.212;ClippingRankSum=0.000;DP=149;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.000;RAW_MQ=536400.00;ReadPosRankSum=3.064 GT:AD:DP:GQ:PL:SB 1/1:2,138,0:140:99:4280,371,0,4286,414,4330:1,1,71,67
chrM 16522 . C <NON_REF> . . END=16561 GT:DP:GQ:MIN_DP:PL 0/0:134:99:108:0,120,1800
chrM 16562 . C <NON_REF> . . END=16571 GT:DP:GQ:MIN_DP:PL 0/0:101:0:97:0,0,0
test/data/16699289_chrM.vcf 0 → 100644
+ 166
− 0
View file @ 317e9316
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test/test-dry-run.yml 0 → 100644
+ 11
− 0
View file @ 317e9316
- name: test-dry-run-GIAB-chrM
tags:
- dry-run
command: >
snakemake -n
--configfile test/config/config-GIAB-chrM.json
--use-singularity
stdout:
contains:
- "Job counts:"
test/test-integration.yml 0 → 100644
+ 14
− 0
View file @ 317e9316
- name: test-integration-GIAB-chrM
tags:
- integration
command: >
snakemake
--configfile test/config/config-GIAB-chrM.json
--use-singularity
--singularity-args ' --containall --bind /tmp'
--cores 1
16699289_coverage.varda 16699289_variants.varda
files:
- path: 16699289_coverage.varda
- path: 16699289_variants.varda
test/test-sanity.yml 0 → 100644
+ 14
− 0
View file @ 317e9316
- name: test-sanity-singularity
tags:
- sanity
command: >
singularity --version
stdout:
contains:
- "singularity version 3"
- name: test-sanity-snakemake
tags:
- sanity
command: >
snakemake --version
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