Mercurial > repos > iuc > happy
changeset 0:5095e751304c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy commit 9ae0037c379b589aa8e0f825820bb4a7c969cdb2"
| author | iuc |
|---|---|
| date | Tue, 25 Jan 2022 11:02:23 +0000 |
| parents | |
| children | 728bd4d000b0 |
| files | hap.py.xml hap.py_macros.xml test-data/chr21.fa test-data/happy.metrics.json test-data/happy.stats.csv test-data/results.tsv test-data/small_NA12878-Freebayes-chr21.vcf test-data/small_NA12878-GATK3-chr21.vcf |
| diffstat | 8 files changed, 3812 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hap.py.xml Tue Jan 25 11:02:23 2022 +0000 @@ -0,0 +1,76 @@ +<tool id="som.py" name="som.py" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> + <description>A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.</description> + + <macros> + <token name="@TOOL_VERSION@">0.3.14</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + + <requirements> + <requirement type="package" version="@TOOL_VERSION@">hap.py</requirement> + </requirements> + + <command detect_errors="exit_code"><![CDATA[ + +#if $reference_genome.source == 'history': + #set $ref_genome = 'reference.fasta' + ln -s -f '${reference_genome.history_item}' $ref_genome; + samtools faidx $ref_genome; +#else: + #set $ref_genome = $reference_genome.index.fields.path +#end if + export HGREF='$ref_genome' && + som.py + '$truth' + '$query' + -r '$ref_genome' + -o 'happy' | sed 's/\s\+/\t/g' | tail -n+2> results.tsv + ]]> + </command> + + <inputs> + <conditional name="reference_genome"> + <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options."> + <option value="indexed" selected="true">Use a built-in genome</option> + <option value="history">Use a genome from history</option> + </param> + <when value="indexed"> + <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team."> + <options from_data_table="fasta_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No genomes are available for the selected input dataset" /> + </options> + </param> + </when> + <when value="history"> + <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" /> + </when> + </conditional> + <param name="truth" type="data" format="vcf" label="ground truth variant calls"/> + <param name="query" type="data" format="vcf" label="query variant calls"/> + </inputs> + + <outputs> + <data name="results" label="${tool.name} on ${on_string}" format="tabular" from_work_dir="results.tsv"/> + <data name="stats" label="${tool.name} on ${on_string}: stats" format="csv" from_work_dir="happy.stats.csv" /> + <data name="metrics" label="${tool.name} on ${on_string}: metrics" format="json" from_work_dir="happy.metrics.json"/> + </outputs> + + <tests> + <test expect_num_outputs="3"> + <param name="source" value="history"/> + <param name="history_item" value="chr21.fa"/> + <param name="truth" value="small_NA12878-Freebayes-chr21.vcf"/> + <param name="query" value="small_NA12878-GATK3-chr21.vcf"/> + + <output name="results" file="results.tsv"/> + <output name="stats" file="happy.stats.csv" compare="sim_size" delta_frac="0.3" /> + <output name="metrics" file="happy.metrics.json" compare="sim_size" delta_frac="0.3" /> + </test> + </tests> + + <help><![CDATA[ + som.py is a tool to perform comparisons only based on chromosome, position, and allele identity. This comparison will not resolve haplotypes and only verify that the same alleles were observed at the same positions (e.g. for comparison of somatic callsets). + ]]></help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hap.py_macros.xml Tue Jan 25 11:02:23 2022 +0000 @@ -0,0 +1,7 @@ +<macros> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">hap.py</xref> + </xrefs> + </xml> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr21.fa Tue Jan 25 11:02:23 2022 +0000 @@ -0,0 +1,1000 @@ +>chr21 +ttcaaaaagagtgtttcaaaactgctctatgaaaaggaatgttcaactct +gtgagttaaataaaagcatcaaaaaaaagtttctgagaatgcttctgtct +agtttttatgtgaagatatttccattttctctataagcctcaaagctgtc +caaatgtccacttgcagatactacaaaaagagtgtttcaaaagtgctcaa +tgaaaaggaatgttcagctctgtgagttaaatgcaaacatcacaaataag +tttctgagaatgcttctgtctagtttttatgggaagataattccgtgtcc +agcgaaggcttcaaagctttcaaaatatccacttgcaaattctacaaaaa +gagtgtttcaaagctgctttatcaaaagaaagtttcaactctgtgagttg +aatgtgcacatcacaaagaagtttctgagaatgccttcagtctggttttt +atgtgaagatattcccttttccaacgaaagcctcgaagctgtccaaatat +ccacttgtaagtgctgcaaaaagagtgtttcaaaactgctacagcaaaag +aaaggtttatctctgtgagttgagtagacacatcaagaagaaatttctga +gaatgcttctgtctagtttttatgtgaagatatttcctttgtcaccatag +gcctccaagccctccaaatgtccacttgcagatgctacaaaaagagtgtt +tcaaaactgctgtatgaaaagaaatgctcaaatctgtgagataaatgcat +acatcacaaagaagtctttgagaatgcttctgtctagtttttatgttaag 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/happy.metrics.json Tue Jan 25 11:02:23 2022 +0000 @@ -0,0 +1,1 @@ +{"runInfo": [{"value": "/usr/local/bin/som.py test-data/small_NA12878-Freebayes-chr21.vcf test-data/small_NA12878-GATK3-chr21.vcf -r test-data/chr21.fa -o happy", "key": "commandline"}], "metrics": [{"data": [{"values": [0, 1, 5], "type": "string", "id": "types", "label": "types"}, {"values": ["indels", "SNVs", "records"], "type": "string", "id": "type", "label": "type"}, {"values": [1, 4, 4], "type": "int64", "id": "total.truth", "label": "total.truth"}, {"values": [1, 3, 4], "type": "int64", "id": "total.query", "label": "total.query"}, {"values": [0, 0, 0], "type": "int64", "id": "tp", "label": "tp"}, {"values": [1, 3, 4], "type": "int64", "id": "fp", "label": "fp"}, {"values": [1, 4, 4], "type": "int64", "id": "fn", "label": "fn"}, {"values": [0, 0, 0], "type": "int64", "id": "unk", "label": "unk"}, {"values": [0, 0, 0], "type": "int64", "id": "ambi", "label": "ambi"}, {"values": [0.0, 0.0, 0.0], "type": "double", "id": "recall", "label": "recall"}, {"values": [0.0, 0.0, 0.0], "type": "double", "id": "recall_lower", "label": "recall_lower"}, {"values": [0.975, 0.6023646356164746, 0.6023646356164746], "type": "double", "id": "recall_upper", "label": "recall_upper"}, {"values": [0.0, 0.0, 0.0], "type": "double", "id": "recall2", "label": "recall2"}, {"values": [0.0, 0.0, 0.0], "type": "double", "id": "precision", "label": "precision"}, {"values": [0.0, 0.0, 0.0], "type": "double", "id": "precision_lower", "label": "precision_lower"}, {"values": [0.975, 0.7075982261787133, 0.6023646356164746], "type": "double", "id": "precision_upper", "label": "precision_upper"}, {"values": [0.0, 0.0, 0.0], "type": "double", "id": "na", "label": "na"}, {"values": [0.0, 0.0, 0.0], "type": "double", "id": "ambiguous", "label": "ambiguous"}, {"values": [49950, 49950, 49950], "type": "int64", "id": "fp.region.size", "label": "fp.region.size"}, {"values": [20.02002002002002, 60.06006006006006, 80.08008008008008], "type": "double", "id": "fp.rate", "label": "fp.rate"}], "properties": [], "type": "Table", "id": "result", "label": "result"}], "version": "", "sampleInfo": [], "name": "som.py.comparison", "parameters": [], "timestamp": "Fri Jan 21 11:08:26 2022", "metadata": {"required": {"version": "", "id": "haplotypes", "module": "som.py", "description": "/usr/local/bin/som.py generated this JSON file via command line /usr/local/bin/som.py test-data/small_NA12878-Freebayes-chr21.vcf test-data/small_NA12878-GATK3-chr21.vcf -r test-data/chr21.fa -o happy"}}} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/happy.stats.csv Tue Jan 25 11:02:23 2022 +0000 @@ -0,0 +1,4 @@ +,type,total.truth,total.query,tp,fp,fn,unk,ambi,recall,recall_lower,recall_upper,recall2,precision,precision_lower,precision_upper,na,ambiguous,fp.region.size,fp.rate,sompyversion,sompycmd +0,indels,1,1,0,1,1,0,0,0.0,0.0,0.975,0.0,0.0,0.0,0.975,0.0,0.0,49950,20.02002002002002,som.py-,/usr/local/bin/som.py test-data/small_NA12878-Freebayes-chr21.vcf test-data/small_NA12878-GATK3-chr21.vcf -r test-data/chr21.fa -o happy +1,SNVs,4,3,0,3,4,0,0,0.0,0.0,0.6023646356164746,0.0,0.0,0.0,0.7075982261787133,0.0,0.0,49950,60.06006006006006,som.py-,/usr/local/bin/som.py test-data/small_NA12878-Freebayes-chr21.vcf test-data/small_NA12878-GATK3-chr21.vcf -r test-data/chr21.fa -o happy +5,records,4,4,0,4,4,0,0,0.0,0.0,0.6023646356164746,0.0,0.0,0.0,0.6023646356164746,0.0,0.0,49950,80.08008008008008,som.py-,/usr/local/bin/som.py test-data/small_NA12878-Freebayes-chr21.vcf test-data/small_NA12878-GATK3-chr21.vcf -r test-data/chr21.fa -o happy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results.tsv Tue Jan 25 11:02:23 2022 +0000 @@ -0,0 +1,4 @@ + type total.truth total.query tp fp fn unk ambi recall recall_lower recall_upper recall2 precision precision_lower precision_upper na ambiguous fp.region.size fp.rate +0 indels 1 1 0 1 1 0 0 0.0 0.0 0.975000 0.0 0.0 0.0 0.975000 0.0 0.0 49950 20.02002 +1 SNVs 4 3 0 3 4 0 0 0.0 0.0 0.602365 0.0 0.0 0.0 0.707598 0.0 0.0 49950 60.06006 +5 records 4 4 0 4 4 0 0 0.0 0.0 0.602365 0.0 0.0 0.0 0.602365 0.0 0.0 49950 80.08008
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_NA12878-Freebayes-chr21.vcf Tue Jan 25 11:02:23 2022 +0000 @@ -0,0 +1,91 @@ +##fileformat=VCFv4.1 +##FILTER=<ID=PASS,Description="All filters passed"> +##fileDate=20150506 +##source=freeBayes v0.9.21-15-g8a06a0b +##reference=/illumina/development/Isis/Genomes/Homo_sapiens/NCBI/GRCh38Decoy/Sequence/WholeGenomeFasta/genome.fa +##phasing=none +##commandline="/home/efritzilas/freebayes/bin/freebayes -f /illumina/development/Isis/Genomes/Homo_sapiens/NCBI/GRCh38Decoy/Sequence/WholeGenomeFasta/genome.fa --stdin" +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> 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partial observations"> +##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> +##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> +##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> +##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> +##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> +##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of 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Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> +##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> +##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> +##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> +##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> +##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> +##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> +##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> 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+##contig=<ID=chr17> +##contig=<ID=chr18> +##contig=<ID=chr19> +##contig=<ID=chr20> +##contig=<ID=chr21> +##contig=<ID=chr22> +##contig=<ID=chrX> +##bcftools_concatCommand=concat -f ConcatVcfList.txt -o WholeGenome.vcf.gz -O z +##bcftools_viewVersion=1.2+htslib-1.2.1 +##bcftools_viewCommand=view '--exclude=INFO/AC == 0' -O z -o WholeGenome-trimmed.vcf.gz ../WholeGenome/WholeGenome.vcf.gz +##bcftools_viewCommand=view -s NA12878 -O z -o /home/pkrusche/NA12878-Freebayes.vcf.gz /illumina/build/platinumgenomes/HG38_Builds/ncbi/CompleteDecoy/bwa/FreeBayes/WholeGenome-trimmed/WholeGenome-trimmed.vcf.gz +##bcftools_viewCommand=view -r chr21 -o NA12878-Freebayes-chr21.vcf.gz -O z NA12878-Freebayes.vcf.gz +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +chr21 5030896 . G A 0.000502376 . AB=0.333333;ABP=3.73412;AC=0;AF=0.21875;AN=2;AO=15;CIGAR=1X;DP=321;DPB=321;DPRA=0.446739;EPP=35.5824;EPPR=3.46446;GTI=3;LEN=1;MEANALT=1;MQM=20.2;MQMR=31.4085;NS=16;NUMALT=1;ODDS=9.12603;PAIRED=0.933333;PAIREDR=0.888889;PAO=0;PQA=0;PQR=0;PRO=0;QA=560;QR=10475;RO=306;RPL=0;RPP=35.5824;RPPR=76.8404;RPR=15;RUN=1;SAF=15;SAP=35.5824;SAR=0;SRF=167;SRP=8.57381;SRR=139;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/0:25:24:868:1:30:0,-5.0019,-54.4453 +chr21 5031107 . A T 3.66575e-05 . AB=0.5;ABP=3.0103;AC=0;AF=0.0294118;AN=2;AO=32;CIGAR=1X;DP=161;DPB=161;DPRA=2.55;EPP=3.28173;EPPR=27.5072;GTI=0;LEN=1;MEANALT=1.06667;MQM=22.5312;MQMR=25.5781;NS=17;NUMALT=1;ODDS=12.616;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=236;QR=4194;RO=128;RPL=15;RPP=3.28173;RPPR=172.657;RPR=17;RUN=1;SAF=0;SAP=72.4974;SAR=32;SRF=41;SRP=38.9075;SRR=87;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/0:15:14:551:1:7:0,-3.81891,-31.6415 +chr21 5031112 . A T 5.97645e-05 . AB=0.4;ABP=5.61607;AC=0;AF=0.0882353;AN=2;AO=30;CIGAR=1X;DP=150;DPB=150;DPRA=2.25641;EPP=3.29983;EPPR=36.7502;GTI=2;LEN=1;MEANALT=1.07692;MQM=23.9333;MQMR=25.3277;NS=17;NUMALT=1;ODDS=12.2549;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=238;QR=3754;RO=119;RPL=16;RPP=3.29983;RPPR=141.127;RPR=14;RUN=1;SAF=0;SAP=68.1545;SAR=30;SRF=34;SRP=50.4725;SRR=85;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/0:13:12:456:1:7:0,-3.21685,-26.7225 +chr21 5031122 . CAC CC,CCC 0.00387406 . AB=0.241379,0.448276;ABP=19.8579,4.35811;AC=0,0;AF=0.0625,0.21875;AN=2;AO=12,38;CIGAR=1M1D1M,1M1X1M;DP=126;DPB=125.667;DPRA=1.87179,2.57143;EPP=14.5915,3.9246;EPPR=11.1853;GTI=8;LEN=1,1;MEANALT=2.11111,2;MQM=23.8333,27.2105;MQMR=24.6912;NS=16;NUMALT=2;ODDS=7.61863;PAIRED=1,0.973684;PAIREDR=0.985294;PAO=1.66667,1.66667;PQA=23,23;PQR=123;PRO=4.66667;QA=114,487;QR=2110;RO=68;RPL=2,21;RPP=14.5915,3.9246;RPPR=49.1222;RPR=10,17;RUN=1,1;SAF=0,0;SAP=29.068,85.5263;SAR=12,38;SRF=23;SRP=18.4661;SRR=45;TYPE=del,snp GT:DP:RO:QR:AO:QA:GL 0/0:13:10:323:1,2:7,14:0,-2.68445,-20.1039,-2.35859,-19.7797,-19.489
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_NA12878-GATK3-chr21.vcf Tue Jan 25 11:02:23 2022 +0000 @@ -0,0 +1,2629 @@ +##fileformat=VCFv4.1 +##FILTER=<ID=PASS,Description="All filters passed"> +##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> +##FILTER=<ID=LowQual,Description="Low quality"> +##FORMAT=<ID=AD,Number=.,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=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=<ID=GenotypeGVCFs,Version=2014.3-3.2.2-7-gf9cba99,Date="Thu May 14 16:14:43 BST 2015",Epoch=1431616483332,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null phone_home=NO_ET gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/illumina/development/Isis/Genomes/Homo_sapiens/NCBI/GRCh38Decoy/Sequence/WholeGenomeFasta/genome.fa 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 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=40 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 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=NA12877_150507_210234.tmp/NA12877.vcf)]), (RodBindingCollection [(RodBinding name=variant2 source=NA12878_150507_210325.tmp/NA12878.vcf)]), (RodBindingCollection [(RodBinding name=variant3 source=NA12879_150507_210442.tmp/NA12879.vcf)]), (RodBindingCollection [(RodBinding name=variant4 source=NA12880_150507_210537.tmp/NA12880.vcf)]), (RodBindingCollection [(RodBinding name=variant5 source=NA12881_150507_210631.tmp/NA12881.vcf)]), (RodBindingCollection [(RodBinding name=variant6 source=NA12882_150507_210900.tmp/NA12882.vcf)]), (RodBindingCollection [(RodBinding name=variant7 source=NA12883_150507_213034.tmp/NA12883.vcf)]), (RodBindingCollection [(RodBinding name=variant8 source=NA12884_150507_220552.tmp/NA12884.vcf)]), (RodBindingCollection [(RodBinding name=variant9 source=NA12885_150507_231013.tmp/NA12885.vcf)]), (RodBindingCollection [(RodBinding name=variant10 source=NA12886_150508_002206.tmp/NA12886.vcf)]), (RodBindingCollection [(RodBinding name=variant11 source=NA12887_150508_025440.tmp/NA12887.vcf)]), (RodBindingCollection [(RodBinding name=variant12 source=NA12888_150508_092328.tmp/NA12888.vcf)]), (RodBindingCollection [(RodBinding name=variant13 source=NA12889_150508_094035.tmp/NA12889.vcf)]), (RodBindingCollection [(RodBinding name=variant14 source=NA12890_150508_094126.tmp/NA12890.vcf)]), (RodBindingCollection [(RodBinding name=variant15 source=NA12891_150508_094432.tmp/NA12891.vcf)]), (RodBindingCollection [(RodBinding name=variant16 source=NA12892_150508_094845.tmp/NA12892.vcf)]), (RodBindingCollection [(RodBinding name=variant17 source=NA12893_150508_100944.tmp/NA12893.vcf)])] out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub includeNonVariantSites=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=25.0 standard_min_confidence_threshold_for_emitting=10.0 max_alternate_alleles=8 input_prior=[] sample_ploidy=2 annotation=[InbreedingCoeff, FisherStrand, QualByDepth, ChromosomeCounts, GenotypeSummaries] dbsnp=(RodBinding name= source=UNBOUND) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> +##GATKCommandLine=<ID=HaplotypeCaller,Version=2014.3-3.2.2-7-gf9cba99,Date="Fri May 08 12:19:14 BST 2015",Epoch=1431083954832,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/illumina/scratch/GATK/results/GATK_WGS/PlatinumGenomes/hg38/Best_Practices/NA12891_150508_094432.tmp/NA12891.realigned.bam] showFullBamList=false read_buffer_size=null phone_home=NO_ET gatk_key=null tag=NA read_filter=[] intervals=[chr1:1-100000000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/illumina/development/Isis/Genomes/Homo_sapiens/NCBI/GRCh38Decoy/Sequence/WholeGenomeFasta/genome.fa 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=6 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=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=128 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"> +##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> +##INFO=<ID=CCC,Number=1,Type=Integer,Description="Number of called chromosomes"> +##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=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=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> +##INFO=<ID=GQ_MEAN,Number=1,Type=Float,Description="Mean of all GQ values"> +##INFO=<ID=GQ_STDDEV,Number=1,Type=Float,Description="Standard deviation of all GQ values"> +##INFO=<ID=HWP,Number=1,Type=Float,Description="P value from test of Hardy Weinberg Equilibrium"> +##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site 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NA12891_150508_094432.tmp/NA12891_chr7.2.vcf NA12891_150508_094432.tmp/NA12891_chr8.1.vcf NA12891_150508_094432.tmp/NA12891_chr8.2.vcf NA12891_150508_094432.tmp/NA12891_chr9.1.vcf NA12891_150508_094432.tmp/NA12891_chr9.2.vcf NA12891_150508_094432.tmp/NA12891_chr10.1.vcf NA12891_150508_094432.tmp/NA12891_chr10.2.vcf NA12891_150508_094432.tmp/NA12891_chr11.1.vcf NA12891_150508_094432.tmp/NA12891_chr11.2.vcf NA12891_150508_094432.tmp/NA12891_chr12.1.vcf NA12891_150508_094432.tmp/NA12891_chr12.2.vcf NA12891_150508_094432.tmp/NA12891_chr13.1.vcf NA12891_150508_094432.tmp/NA12891_chr13.2.vcf NA12891_150508_094432.tmp/NA12891_chr14.1.vcf NA12891_150508_094432.tmp/NA12891_chr14.2.vcf NA12891_150508_094432.tmp/NA12891_chr15.1.vcf NA12891_150508_094432.tmp/NA12891_chr15.2.vcf NA12891_150508_094432.tmp/NA12891_chr16.1.vcf NA12891_150508_094432.tmp/NA12891_chr17.1.vcf NA12891_150508_094432.tmp/NA12891_chr18.1.vcf NA12891_150508_094432.tmp/NA12891_chr19.1.vcf 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