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Merge VCF header lines with VCFHeaderLineCount.INTEGER correctly.
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adam-core/src/test/resources/invalid/truth_small_variants.vcf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| ##fileformat=VCFv4.2 | ||
| ##fileDate=20160824 | ||
| ##CL=vcffilter -i filtered-phase-transfer.vcf.gz -o - --javascript "ensureFormatHeader(\"##FORMAT=<ID=PS,Number=1,Type=String,Description=\\\"Phase set for GT\\\">\"); function record() {if(INTEGRATION.GT==\"1/1\") { INTEGRATION.IPS=\".\"; INTEGRATION.PS=\"HOMVAR\"; INTEGRATION.GT=\"1|1\";} else {if((INTEGRATION.GT==\"0/1\" || INTEGRATION.GT==\"1/2\" || INTEGRATION.GT==\"2/1\" || INTEGRATION.GT==\"1/0\") ) {if(INTEGRATION.IPS.length>1) {INTEGRATION.PS=INTEGRATION.IPS; INTEGRATION.GT=INTEGRATION.IGT;} else {INTEGRATION.PS=\".\";};} else { if((INTEGRATION.IPS.length<2)) { INTEGRATION.IPS=\".\";} INTEGRATION.PS=\"PATMAT\";};};}" | ||
| ##RUN-ID=16dacf15-fdc9-4199-84bd-723ea8bcddef | ||
| ##contig=<ID=chr1,length=248956422> | ||
| ##contig=<ID=chr2,length=242193529> | ||
| ##contig=<ID=chr3,length=198295559> | ||
| ##contig=<ID=chr4,length=190214555> | ||
| ##contig=<ID=chr5,length=181538259> | ||
| ##contig=<ID=chr6,length=170805979> | ||
| ##contig=<ID=chr7,length=159345973> | ||
| ##contig=<ID=chr8,length=145138636> | ||
| ##contig=<ID=chr9,length=138394717> | ||
| ##contig=<ID=chr10,length=133797422> | ||
| ##contig=<ID=chr11,length=135086622> | ||
| ##contig=<ID=chr12,length=133275309> | ||
| ##contig=<ID=chr13,length=114364328> | ||
| ##contig=<ID=chr14,length=107043718> | ||
| ##contig=<ID=chr15,length=101991189> | ||
| ##contig=<ID=chr16,length=90338345> | ||
| ##contig=<ID=chr17,length=83257441> | ||
| ##contig=<ID=chr18,length=80373285> | ||
| ##contig=<ID=chr19,length=58617616> | ||
| ##contig=<ID=chr20,length=64444167> | ||
| ##contig=<ID=chr21,length=46709983> | ||
| ##contig=<ID=chr22,length=50818468> | ||
| ##contig=<ID=chrX,length=156040895> | ||
| ##contig=<ID=chrY,length=57227415> | ||
| ##contig=<ID=chrM,length=16569> | ||
| ##FILTER=<ID=GQlessthan70,Description="Sum of GQ for datasets with this genotype less than 70"> | ||
| ##FILTER=<ID=allfilteredanddisagree,Description="All callsets have this call filtered or outside the callable regions and they have discordant genotypes or variant calls"> | ||
| ##FILTER=<ID=allfilteredbutagree,Description="All callsets have this call filtered or outside the callable regions but they have the same genotype"> | ||
| ##FILTER=<ID=discordantunfiltered,Description="Callsets with unfiltered calls have discordant genotypes or variant calls"> | ||
| ##FILTER=<ID=discordanthet,Description="Filtered calls where a passing call is het and a high GQ but filtered call is hom var, since often the het is wrong"> | ||
| ##FILTER=<ID=questionableindel,Description="Filtered calls where some callsets have a filtered indel larger than 10bp and another dataset has an implied homozygous reference call"> | ||
| ##FILTER=<ID=cgonly,Description="Filtered calls where only Complete Genomics had this call and it was completely missing from any other callset"> | ||
| ##FILTER=<ID=alleleimbalance,Description="Filtered calls where the net allele balance for unfiltered datasets is <0.2 or >0.8"> | ||
| ##FILTER=<ID=overlappingcall,Description="Filtered sites that are within 50bp of another passing call but none of the callsets that support the 2 calls match"> | ||
| ##INFO=<ID=DPSum,Number=1,Type=Integer,Description="Total read depth summed across all datasets, excluding MQ0 reads"> | ||
| ##INFO=<ID=platforms,Number=1,Type=Integer,Description="Number of different platforms for which at least one callset called this genotype, whether filtered or not"> | ||
| ##INFO=<ID=platformnames,Number=.,Type=String,Description="Names of platforms for which at least one callset called this genotype, whether filtered or not"> | ||
| ##INFO=<ID=platformbias,Number=.,Type=String,Description="Names of platforms that have reads containing a variant at this location, but the high-confidence call is homozygous reference, indicating that there is a potential bias."> | ||
| ##INFO=<ID=datasets,Number=1,Type=Integer,Description="Number of different datasets for which at least one callset called this genotype, whether filtered or not"> | ||
| ##INFO=<ID=datasetnames,Number=.,Type=String,Description="Names of datasets for which at least one callset called this genotype, whether filtered or not"> | ||
| ##INFO=<ID=datasetsmissingcall,Number=.,Type=Integer,Description="Names of datasets that are missing a call or have an incorrect call at this location, and the high-confidence call is a variant"> | ||
| ##INFO=<ID=callsets,Number=1,Type=Integer,Description="Number of different callsets that called this genotype, whether filtered or not"> | ||
| ##INFO=<ID=callsetnames,Number=.,Type=String,Description="Names of callsets that called this genotype, whether filtered or not"> | ||
| ##INFO=<ID=varType,Number=1,Type=String,Description="Type of variant"> | ||
| ##INFO=<ID=filt,Number=.,Type=String,Description="List of callsets that had this call filtered."> | ||
| ##INFO=<ID=callable,Number=.,Type=String,Description="List of callsets that had this call in a region with low coverage of high MQ reads."> | ||
| ##INFO=<ID=difficultregion,Number=.,Type=String,Description="List of difficult region bed files containing this call."> | ||
| ##INFO=<ID=arbitrated,Number=1,Type=String,Description="TRUE if callsets had discordant calls so that arbitration was needed."> | ||
| ##INFO=<ID=callsetwiththisuniqgenopassing,Number=.,Type=String,Description="Callset that uniquely calls the PASSing genotype in GT when 2+ PASSing callsets support a different genotype."> | ||
| ##INFO=<ID=callsetwithotheruniqgenopassing,Number=.,Type=String,Description="Callset that uniquely calls a PASSing genotype different from GT when 2+ PASSing callsets support the genotype in GT."> | ||
| ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth summed across all datasets, excluding MQ0 reads"> | ||
| ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Net Genotype quality across all datasets, calculated from GQ scores of callsets supporting the consensus GT, using only one callset from each dataset"> | ||
| ##FORMAT=<ID=ADALL,Number=R,Type=Integer,Description="Net allele depths across all datasets"> | ||
| ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Net allele depths across all unfiltered datasets with called genotype"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Consensus Genotype across all datasets with called genotype"> | ||
| ##FORMAT=<ID=IGT,Number=1,Type=String,Description="Original input genotype"> | ||
| ##FORMAT=<ID=IPS,Number=1,Type=String,Description="Phase set for IGT"> | ||
| ##FORMAT=<ID=PS,Number=1,Type=String,Description="Phase set for GT"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT INTEGRATION | ||
| chr1 817186 . G A 50 PASS platforms=3;platformnames=Illumina,CG,Solid;datasets=3;datasetnames=HiSeqPE300x,CGnormal,SolidSE75bp;callsets=4;callsetnames=HiSeqPE300xGATK,CGnormal,HiSeqPE300xfreebayes,SolidSE75GATKHC;datasetsmissingcall=10XChromium,IonExome,SolidPE50x50bp;callable=CS_HiSeqPE300xGATK_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_SolidSE75GATKHC_filt GT:DP:ADALL:AD:GQ:IGT:IPS:PS 1|1:823:0,381:78,454:283:1/1:.:PATMAT | ||
| chr1 817341 . A G 50 PASS platforms=3;platformnames=Illumina,CG,Solid;datasets=4;datasetnames=HiSeqPE300x,CGnormal,SolidPE50x50bp,SolidSE75bp;callsets=5;callsetnames=HiSeqPE300xGATK,CGnormal,HiSeqPE300xfreebayes,SolidPE50x50GATKHC,SolidSE75GATKHC;datasetsmissingcall=10XChromium,IonExome;callable=CS_HiSeqPE300xGATK_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_SolidPE50x50GATKHC_filt GT:DP:ADALL:AD:GQ:IGT:IPS:PS 1|1:584:0,255:107,342:327:1/1:.:PATMAT | ||
| chr1 817889 . C G 50 PASS platforms=2;platformnames=Illumina,CG;datasets=2;datasetnames=HiSeqPE300x,CGnormal;callsets=3;callsetnames=HiSeqPE300xGATK,CGnormal,HiSeqPE300xfreebayes;datasetsmissingcall=10XChromium,IonExome,SolidPE50x50bp,SolidSE75bp;callable=CS_HiSeqPE300xGATK_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable GT:DP:ADALL:AD:GQ:IGT:IPS:PS 1|1:361:0,146:74,220:209:1/1:.:PATMAT | ||
| chr1 818025 . C A 50 PASS platforms=2;platformnames=Illumina,CG;datasets=2;datasetnames=HiSeqPE300x,CGnormal;callsets=3;callsetnames=HiSeqPE300xGATK,CGnormal,HiSeqPE300xfreebayes;datasetsmissingcall=10XChromium,IonExome,SolidPE50x50bp,SolidSE75bp;callable=CS_HiSeqPE300xGATK_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_HiSeqPE300xGATK_filt,CS_HiSeqPE300xfreebayes_filt GT:DP:ADALL:AD:GQ:IGT:IPS:PS 1|1:283:0,118:43,43:219:1/1:.:PATMAT | ||
| chr1 818802 . A G 50 PASS platforms=2;platformnames=Illumina,Solid;datasets=2;datasetnames=HiSeqPE300x,SolidSE75bp;callsets=3;callsetnames=HiSeqPE300xGATK,HiSeqPE300xfreebayes,SolidSE75GATKHC;datasetsmissingcall=CGnormal,10XChromium,IonExome,SolidPE50x50bp;callable=CS_HiSeqPE300xGATK_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_HiSeqPE300xfreebayes_filt,CS_SolidSE75GATKHC_filt GT:DP:ADALL:AD:GQ:IGT:IPS:PS 1|1:432:0,205:0,202:108:1|1:818802_A_G:PATMAT | ||
| chr1 818812 . A G 50 PASS platforms=2;platformnames=Illumina,Solid;datasets=2;datasetnames=HiSeqPE300x,SolidSE75bp;callsets=3;callsetnames=HiSeqPE300xGATK,HiSeqPE300xfreebayes,SolidSE75GATKHC;datasetsmissingcall=CGnormal,10XChromium,IonExome,SolidPE50x50bp;callable=CS_HiSeqPE300xGATK_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_HiSeqPE300xfreebayes_filt,CS_SolidSE75GATKHC_filt GT:DP:ADALL:AD:GQ:IGT:IPS:PS 1|1:412:0,192:0,190:108:1|1:818802_A_G:PATMAT | ||
| chr1 818954 . T C 50 PASS platforms=3;platformnames=Illumina,CG,Solid;datasets=3;datasetnames=HiSeqPE300x,CGnormal,SolidPE50x50bp;callsets=4;callsetnames=HiSeqPE300xGATK,CGnormal,HiSeqPE300xfreebayes,SolidPE50x50GATKHC;datasetsmissingcall=10XChromium,IonExome,SolidSE75bp;callable=CS_HiSeqPE300xGATK_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_CGnormal_filt,CS_SolidPE50x50GATKHC_filt GT:DP:ADALL:AD:GQ:IGT:IPS 1|1:621:0,250:0,246:233:1/1:. |
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