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feat: implement "seqvars ingest" command (#199)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,144 @@ | ||
| ##fileformat=VCFv4.2 | ||
| ##FILTER=<ID=PASS,Description="All filters passed"> | ||
| ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths (counting only informative reads out of the total reads) for the ref and alt alleles in the order listed"> | ||
| ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions for 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=DN,Number=1,Type=String,Description="Possible values are 'Inherited', 'DeNovo' or 'LowDQ'. Threshold for passing de novo call: SNPs: 0.05, INDELs: 0.02"> | ||
| ##FORMAT=<ID=DPL,Number=.,Type=Integer,Description="Normalized, Phred-scaled likelihoods used for DQ calculation"> | ||
| ##FORMAT=<ID=DQ,Number=1,Type=Float,Description="De novo quality"> | ||
| ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> | ||
| ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> | ||
| ##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample filter, 'PASS' indicates that all filters have passed for this sample"> | ||
| ##FORMAT=<ID=GP,Number=G,Type=Float,Description="Phred-scaled posterior probabilities for genotypes as defined in the VCF specification"> | ||
| ##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=PP,Number=G,Type=Integer,Description="Phred-scaled posterior genotype probabilities using pedigree prior probabilities"> | ||
| ##FORMAT=<ID=PS,Number=1,Type=Integer,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=SQ,Number=A,Type=Float,Description="Somatic quality"> | ||
| ##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=DP,Number=1,Type=Integer,Description="Approximate read depth (informative and non-informative); some reads may have been filtered based on mapq etc."> | ||
| ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> | ||
| ##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=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> | ||
| ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> | ||
| ##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> | ||
| ##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> | ||
| ##INFO=<ID=FractionInformativeReads,Number=1,Type=Float,Description="The fraction of informative reads out of the total reads"> | ||
| ##FILTER=<ID=DRAGENSnpHardQUAL,Description="Set if true:QUAL < 10.41"> | ||
| ##FILTER=<ID=DRAGENIndelHardQUAL,Description="Set if true:QUAL < 7.83"> | ||
| ##FILTER=<ID=LowDepth,Description="Set if true:DP <= 1"> | ||
| ##FILTER=<ID=PloidyConflict,Description="Genotype call from variant caller not consistent with chromosome ploidy"> | ||
| ##FILTER=<ID=DRAGENHardQUAL,Description="Set if true:QUAL < 10.4139"> | ||
| ##FILTER=<ID=LowGQ,Description="Set if true:GQ = 0"> | ||
| ##FILTER=<ID=lod_fstar,Description="Variant does not meet likelihood threshold (default threshold is 6.3)"> | ||
| ##FILTER=<ID=base_quality,Description="Site filtered because median base quality of alt reads at this locus does not meet threshold"> | ||
| ##FILTER=<ID=filtered_reads,Description="Site filtered because too large a fraction of reads have been filtered out"> | ||
| ##FILTER=<ID=fragment_length,Description="Site filtered because absolute difference between the median fragment length of alt reads and median fragment length of ref reads at this locus exceeds threshold"> | ||
| ##FILTER=<ID=low_depth,Description="Site filtered because the read depth is too low"> | ||
| ##FILTER=<ID=low_frac_info_reads,Description="Site filtered because the fraction of informative reads is below threshold"> | ||
| ##FILTER=<ID=low_normal_depth,Description="Site filtered because the normal sample read depth is too low"> | ||
| ##FILTER=<ID=long_indel,Description="Site filtered because the indel length is too long"> | ||
| ##FILTER=<ID=mapping_quality,Description="Site filtered because median mapping quality of alt reads at this locus does not meet threshold"> | ||
| ##FILTER=<ID=multiallelic,Description="Site filtered because more than two alt alleles pass tumor LOD"> | ||
| ##FILTER=<ID=non_homref_normal,Description="Site filtered because the normal sample genotype is not homozygous reference"> | ||
| ##FILTER=<ID=no_reliable_supporting_read,Description="Site filtered because no reliable supporting somatic read exists"> | ||
| ##FILTER=<ID=panel_of_normals,Description="Seen in at least one sample in the panel of normals vcf"> | ||
| ##FILTER=<ID=read_position,Description="Site filtered because median of distances between start/end of read and this locus is below threshold"> | ||
| ##FILTER=<ID=RMxNRepeatRegion,Description="Site filtered because all or part of the variant allele is a repeat of the reference"> | ||
| ##FILTER=<ID=str_contraction,Description="Site filtered due to suspected PCR error where the alt allele is one repeat unit less than the reference"> | ||
| ##FILTER=<ID=too_few_supporting_reads,Description="Site filtered because there are too few supporting reads in the tumor sample"> | ||
| ##FILTER=<ID=weak_evidence,Description="Somatic variant score does not meet threshold"> | ||
| ##contig=<ID=1,length=249250621> | ||
| ##contig=<ID=2,length=243199373> | ||
| ##contig=<ID=3,length=198022430> | ||
| ##contig=<ID=4,length=191154276> | ||
| ##contig=<ID=5,length=180915260> | ||
| ##contig=<ID=6,length=171115067> | ||
| ##contig=<ID=7,length=159138663> | ||
| ##contig=<ID=8,length=146364022> | ||
| ##contig=<ID=9,length=141213431> | ||
| ##contig=<ID=10,length=135534747> | ||
| ##contig=<ID=11,length=135006516> | ||
| ##contig=<ID=12,length=133851895> | ||
| ##contig=<ID=13,length=115169878> | ||
| ##contig=<ID=14,length=107349540> | ||
| ##contig=<ID=15,length=102531392> | ||
| ##contig=<ID=16,length=90354753> | ||
| ##contig=<ID=17,length=81195210> | ||
| ##contig=<ID=18,length=78077248> | ||
| ##contig=<ID=19,length=59128983> | ||
| ##contig=<ID=20,length=63025520> | ||
| ##contig=<ID=21,length=48129895> | ||
| ##contig=<ID=22,length=51304566> | ||
| ##contig=<ID=X,length=155270560> | ||
| ##contig=<ID=Y,length=59373566> | ||
| ##contig=<ID=MT,length=16569> | ||
| ##contig=<ID=GL000207.1,length=4262> | ||
| ##contig=<ID=GL000226.1,length=15008> | ||
| ##contig=<ID=GL000229.1,length=19913> | ||
| ##contig=<ID=GL000231.1,length=27386> | ||
| ##contig=<ID=GL000210.1,length=27682> | ||
| ##contig=<ID=GL000239.1,length=33824> | ||
| ##contig=<ID=GL000235.1,length=34474> | ||
| ##contig=<ID=GL000201.1,length=36148> | ||
| ##contig=<ID=GL000247.1,length=36422> | ||
| ##contig=<ID=GL000245.1,length=36651> | ||
| ##contig=<ID=GL000197.1,length=37175> | ||
| ##contig=<ID=GL000203.1,length=37498> | ||
| ##contig=<ID=GL000246.1,length=38154> | ||
| ##contig=<ID=GL000249.1,length=38502> | ||
| ##contig=<ID=GL000196.1,length=38914> | ||
| ##contig=<ID=GL000248.1,length=39786> | ||
| ##contig=<ID=GL000244.1,length=39929> | ||
| ##contig=<ID=GL000238.1,length=39939> | ||
| ##contig=<ID=GL000202.1,length=40103> | ||
| ##contig=<ID=GL000234.1,length=40531> | ||
| ##contig=<ID=GL000232.1,length=40652> | ||
| ##contig=<ID=GL000206.1,length=41001> | ||
| ##contig=<ID=GL000240.1,length=41933> | ||
| ##contig=<ID=GL000236.1,length=41934> | ||
| ##contig=<ID=GL000241.1,length=42152> | ||
| ##contig=<ID=GL000243.1,length=43341> | ||
| ##contig=<ID=GL000242.1,length=43523> | ||
| ##contig=<ID=GL000230.1,length=43691> | ||
| ##contig=<ID=GL000237.1,length=45867> | ||
| ##contig=<ID=GL000233.1,length=45941> | ||
| ##contig=<ID=GL000204.1,length=81310> | ||
| ##contig=<ID=GL000198.1,length=90085> | ||
| ##contig=<ID=GL000208.1,length=92689> | ||
| ##contig=<ID=GL000191.1,length=106433> | ||
| ##contig=<ID=GL000227.1,length=128374> | ||
| ##contig=<ID=GL000228.1,length=129120> | ||
| ##contig=<ID=GL000214.1,length=137718> | ||
| ##contig=<ID=GL000221.1,length=155397> | ||
| ##contig=<ID=GL000209.1,length=159169> | ||
| ##contig=<ID=GL000218.1,length=161147> | ||
| ##contig=<ID=GL000220.1,length=161802> | ||
| ##contig=<ID=GL000213.1,length=164239> | ||
| ##contig=<ID=GL000211.1,length=166566> | ||
| ##contig=<ID=GL000199.1,length=169874> | ||
| ##contig=<ID=GL000217.1,length=172149> | ||
| ##contig=<ID=GL000216.1,length=172294> | ||
| ##contig=<ID=GL000215.1,length=172545> | ||
| ##contig=<ID=GL000205.1,length=174588> | ||
| ##contig=<ID=GL000219.1,length=179198> | ||
| ##contig=<ID=GL000224.1,length=179693> | ||
| ##contig=<ID=GL000223.1,length=180455> | ||
| ##contig=<ID=GL000195.1,length=182896> | ||
| ##contig=<ID=GL000212.1,length=186858> | ||
| ##contig=<ID=GL000222.1,length=186861> | ||
| ##contig=<ID=GL000200.1,length=187035> | ||
| ##contig=<ID=GL000193.1,length=189789> | ||
| ##contig=<ID=GL000194.1,length=191469> | ||
| ##contig=<ID=GL000225.1,length=211173> | ||
| ##contig=<ID=GL000192.1,length=547496> | ||
| ##contig=<ID=NC_007605,length=171823> | ||
| ##contig=<ID=hs37d5,length=35477943> | ||
| ##reference=file:///staging/human/reference/hs37d5/hs37d5.fa.k_21.f_16.m_149/reference.bin | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT INDEX PARENT_B PARENT_A | ||
| MT 73 . A G . PASS DP=7407;MQ=229.88 GT:AD:AF:DP:FT:SQ:F1R2:F2R1 0/0:2831,6:0.002:1919:PASS:99:.:. 1/1:0,2032:1:2032:PASS:98.13:0,921:0,1111 0/0:4731,17:0.004:3115:PASS:99:.:. |
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