Mercurial > repos > iuc > tbvcfreport

comparison test-data/rif_resistant.vcf @ 3:42818629ec4c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
author iuc
date Fri, 31 May 2024 20:06:49 +0000
parents 02d81b994ef5
children
comparison
equal deleted inserted replaced
2:4934c0ac6197 3:42818629ec4c
1 ##fileformat=VCFv4.2 1 ##fileformat=VCFv4.2
2 ##FILTER=<ID=PASS,Description="All filters passed"> 2 ##FILTER=<ID=PASS,Description="All filters passed">
3 ##bcftoolsVersion=1.9+htslib-1.9 3 ##fileDate=20240531
4 ##bcftoolsCommand=mpileup --fasta-ref /home/pvh/Data/fasta/Mycobacterium_tuberculosis_h37rv.GCA_000195955.2.29.dna.chromosome.Chromosome.fa rif_resistant.bam 4 ##source=freeBayes v1.3.2-dirty
5 ##reference=file:///home/pvh/Data/fasta/Mycobacterium_tuberculosis_h37rv.GCA_000195955.2.29.dna.chromosome.Chromosome.fa 5 ##reference=reference/ref.fa
6 ##contig=<ID=MT_H37RV_BRD_V5,length=4411532> 6 ##contig=<ID=Chromosome,length=4411532>
7 ##ALT=<ID=*,Description="Represents allele(s) other than observed."> 7 ##phasing=none
8 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 8 ##commandline="freebayes -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam --region Chromosome:0-1495040"
9 ##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel"> 9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
10 ##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel"> 10 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
11 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> 11 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
12 ##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> 12 ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
13 ##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)"> 13 ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
14 ##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)"> 14 ##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
15 ##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)"> 15 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
16 ##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
17 ##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
18 ##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
19 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
20 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 16 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
21 ##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)"> 17 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
22 ##INFO=<ID=AF2,Number=1,Type=Float,Description="Max-likelihood estimate of the first and second group ALT allele frequency (assuming HWE)"> 18 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
23 ##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)"> 19 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
24 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads"> 20 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
25 ##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same"> 21 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
26 ##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias"> 22 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
27 ##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies"> 23 ##bcftools_viewVersion=1.13+htslib-1.13
28 ##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3"> 24 ##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Fri May 31 19:43:23 2024
29 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases"> 25 ##bcftools_annotateVersion=1.13+htslib-1.13
30 ##bcftools_callVersion=1.9+htslib-1.9 26 ##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Fri May 31 19:43:24 2024
31 ##bcftools_callCommand=call --ploidy 1 -c -v rif_resistant.mpileup; Date=Tue Apr 2 06:47:33 2019 27 ##SnpEffVersion="5.0e (build 2021-03-09 06:01), by Pablo Cingolani"
32 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT rif_resistant.bam 28 ##SnpEffCmd="SnpEff -noStats -no-downstream -no-upstream -no-utr ref snps.filt.vcf "
33 MT_H37RV_BRD_V5 15890 . G A 225.007 . DP=58;VDB=0.0163018;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,29,24;MQ=60;FQ=-999 GT:PL 1:255,0 29 ##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">
34 MT_H37RV_BRD_V5 154990 . G T 225.007 . DP=57;VDB=0.997362;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,18,38;MQ=60;FQ=-999 GT:PL 1:255,0 30 ##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
35 MT_H37RV_BRD_V5 346693 . G T 225.007 . DP=27;VDB=0.365109;SGB=-0.692976;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,14,12;MQ=60;FQ=-999 GT:PL 1:255,0 31 ##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
36 MT_H37RV_BRD_V5 449194 . G A 225.007 . DP=29;VDB=0.387982;SGB=-0.692976;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,5,21;MQ=60;FQ=-999 GT:PL 1:255,0 32 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT rif_resistant_fastq_gz
37 MT_H37RV_BRD_V5 497491 . G A 225.007 . DP=78;VDB=0.57291;SGB=-0.693147;MQSB=0.99133;MQ0F=0;AF1=1;AC1=1;DP4=0,0,53,24;MQ=60;FQ=-999 GT:PL 1:255,0 33 Chromosome 15890 . G A 1500.92 . AB=0;AO=48;DP=48;QA=1704;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0014c|GENE_Rv0014c|transcript|TRANSCRIPT_Rv0014c|protein_coding|1/1|c.1581C>T|p.Ser527Ser|1581/1881|1581/1881|527/626|| GT:DP:RO:QR:AO:QA:GL 1/1:48:0:0:48:1704:-153.63,-14.4494,0
38 MT_H37RV_BRD_V5 761110 . A T 225.007 . DP=59;VDB=0.35459;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,25,32;MQ=60;FQ=-999 GT:PL 1:255,0 34 Chromosome 154990 . G T 1358.62 . AB=0;AO=45;DP=45;QA=1558;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0127|GENE_Rv0127|transcript|TRANSCRIPT_Rv0127|protein_coding|1/1|c.759G>T|p.Arg253Arg|759/1368|759/1368|253/455|| GT:DP:RO:QR:AO:QA:GL 1/1:45:0:0:45:1558:-140.494,-13.5464,0
39 MT_H37RV_BRD_V5 763031 . T C 225.007 . DP=85;VDB=0.401561;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,38,46;MQ=60;FQ=-999 GT:PL 1:255,0 35 Chromosome 346693 . G T 635.034 . AB=0;AO=20;DP=20;QA=729;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0284|GENE_Rv0284|transcript|TRANSCRIPT_Rv0284|protein_coding|1/1|c.1059G>T|p.Ser353Ser|1059/3993|1059/3993|353/1330|| GT:DP:RO:QR:AO:QA:GL 1/1:20:0:0:20:729:-65.9317,-6.0206,0
40 MT_H37RV_BRD_V5 811753 . C T 225.007 . DP=55;VDB=0.241716;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,27,24;MQ=60;FQ=-999 GT:PL 1:255,0 36 Chromosome 449194 . G A 651.409 . AB=0;AO=23;DP=23;QA=782;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0372c|GENE_Rv0372c|transcript|TRANSCRIPT_Rv0372c|protein_coding|1/1|c.192C>T|p.Gly64Gly|192/756|192/756|64/251|| GT:DP:RO:QR:AO:QA:GL 1/1:23:0:0:23:782:-70.6929,-6.92369,0
41 MT_H37RV_BRD_V5 1565566 . C T 225.007 . DP=52;VDB=0.650985;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,13,36;MQ=60;FQ=-999 GT:PL 1:255,0 37 Chromosome 497491 . G A 1816.74 . AB=0;AO=56;DP=56;QA=2057;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0411c|GENE_Rv0411c|transcript|TRANSCRIPT_Rv0411c|protein_coding|1/1|c.810C>T|p.Asp270Asp|810/987|810/987|270/328|| GT:DP:RO:QR:AO:QA:GL 1/1:56:0:0:56:2057:-185.366,-16.8577,0
42 MT_H37RV_BRD_V5 1833729 . TCCCC TCCCCCC 12.7055 . INDEL;IDV=1;IMF=1;DP=1;SGB=-0.379885;MQ0F=0;AF1=1;AC1=1;DP4=0,0,0,1;MQ=54;FQ=-999 GT:PL 1:50,3,0 38 Chromosome 761110 . A T 1500.1 . AB=0;AO=47;DP=48;QA=1701;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0667|GENE_Rv0667|transcript|TRANSCRIPT_Rv0667|protein_coding|1/1|c.1304A>T|p.Asp435Val|1304/3519|1304/3519|435/1172|| GT:DP:RO:QR:AO:QA:GL 1/1:48:0:0:47:1701:-153.05,-14.1484,0
43 MT_H37RV_BRD_V5 1834177 . A C 225.007 . DP=76;VDB=0.880419;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,42,29;MQ=60;FQ=-999 GT:PL 1:255,0 39 Chromosome 811753 . C T 1585.34 . AB=0;AO=48;DP=48;QA=1796;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0715|GENE_Rv0715|transcript|TRANSCRIPT_Rv0715|protein_coding|1/1|c.12C>T|p.His4His|12/318|12/318|4/105|| GT:DP:RO:QR:AO:QA:GL 1/1:48:0:0:48:1796:-161.892,-14.4494,0
44 MT_H37RV_BRD_V5 1849051 . C T 225.007 . DP=86;VDB=0.199205;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,38,45;MQ=60;FQ=-999 GT:PL 1:255,0 40 Chromosome 1565566 . C T 1332.75 . AB=0;AO=43;DP=43;QA=1534;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1391|GENE_Rv1391|transcript|TRANSCRIPT_Rv1391|protein_coding|1/1|c.126C>T|p.Pro42Pro|126/1257|126/1257|42/418|| GT:DP:RO:QR:AO:QA:GL 1/1:43:0:0:43:1534:-138.344,-12.9443,0
45 MT_H37RV_BRD_V5 2505085 . G A 225.007 . DP=48;VDB=0.280048;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,32,13;MQ=60;FQ=-999 GT:PL 1:255,0 41 Chromosome 1834177 . A C 1769.09 . AB=0;AO=54;DP=54;QA=2006;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv1630|GENE_Rv1630|transcript|TRANSCRIPT_Rv1630|protein_coding|1/1|c.636A>C|p.Arg212Arg|636/1446|636/1446|212/481|| GT:DP:RO:QR:AO:QA:GL 1/1:54:0:0:54:2006:-180.776,-16.2556,0
46 MT_H37RV_BRD_V5 2543395 . T C 225.007 . DP=88;VDB=0.167176;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,37,46;MQ=60;FQ=-999 GT:PL 1:255,0 42 Chromosome 1849051 . C T 2143.76 . AB=0;AO=65;DP=65;QA=2415;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1640c|GENE_Rv1640c|transcript|TRANSCRIPT_Rv1640c|protein_coding|1/1|c.2985G>A|p.Pro995Pro|2985/3519|2985/3519|995/1172|| GT:DP:RO:QR:AO:QA:GL 1/1:65:0:0:65:2415:-217.563,-19.567,0
47 MT_H37RV_BRD_V5 2640807 . G A 225.007 . DP=55;VDB=0.218547;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,29,21;MQ=60;FQ=-999 GT:PL 1:255,0 43 Chromosome 2505085 . G A 1199.98 . AB=0;AO=39;DP=39;QA=1425;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2231c|GENE_Rv2231c|transcript|TRANSCRIPT_Rv2231c|protein_coding|1/1|c.615C>T|p.Ala205Ala|615/1095|615/1095|205/364|| GT:DP:RO:QR:AO:QA:GL 1/1:39:0:0:39:1425:-128.53,-11.7402,0
48 MT_H37RV_BRD_V5 2775361 . C T 225.007 . DP=99;VDB=0.0864314;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,46,44;MQ=60;FQ=-999 GT:PL 1:255,0 44 Chromosome 2543395 . T C 1871.23 . AB=0;AO=58;DP=58;QA=2110;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv2268c|GENE_Rv2268c|transcript|TRANSCRIPT_Rv2268c|protein_coding|1/1|c.882A>G|p.Glu294Glu|882/1470|882/1470|294/489|| GT:DP:RO:QR:AO:QA:GL 1/1:58:0:0:58:2110:-190.142,-17.4597,0
49 MT_H37RV_BRD_V5 2789798 . G T 225.007 . DP=72;VDB=0.231858;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,33,35;MQ=60;FQ=-999 GT:PL 1:255,0 45 Chromosome 2640807 . G A 1341.77 . AB=0;AO=43;DP=43;QA=1519;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2357c|GENE_Rv2357c|transcript|TRANSCRIPT_Rv2357c|protein_coding|1/1|c.258C>T|p.Val86Val|258/1392|258/1392|86/463|| GT:DP:RO:QR:AO:QA:GL 1/1:43:0:0:43:1519:-136.983,-12.9443,0
50 MT_H37RV_BRD_V5 3477942 . A G 225.007 . DP=100;VDB=0.912557;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,45,52;MQ=60;FQ=-999 GT:PL 1:255,0 46 Chromosome 2775361 . C T 2221.3 . AB=0;AO=69;DP=69;QA=2506;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2472|GENE_Rv2472|transcript|TRANSCRIPT_Rv2472|protein_coding|1/1|c.90C>T|p.Arg30Arg|90/294|90/294|30/97|| GT:DP:RO:QR:AO:QA:GL 1/1:69:0:0:69:2506:-225.745,-20.7711,0
51 MT_H37RV_BRD_V5 3587446 . G A 225.007 . DP=59;VDB=0.0078857;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,33,24;MQ=60;FQ=-999 GT:PL 1:255,0 47 Chromosome 2789798 . G T 2050.68 . AB=0;AO=62;DP=62;QA=2312;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2483c|GENE_Rv2483c|transcript|TRANSCRIPT_Rv2483c|protein_coding|1/1|c.1225C>A|p.Arg409Arg|1225/1743|1225/1743|409/580|| GT:DP:RO:QR:AO:QA:GL 1/1:62:0:0:62:2312:-208.29,-18.6639,0
52 MT_H37RV_BRD_V5 4254431 . G A 225.007 . DP=58;VDB=0.120561;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,25,33;MQ=60;FQ=-999 GT:PL 1:255,0 48 Chromosome 3477942 . A G 2414.91 . AB=0;AO=75;DP=75;QA=2721;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv3109|GENE_Rv3109|transcript|TRANSCRIPT_Rv3109|protein_coding|1/1|c.294A>G|p.Thr98Thr|294/1080|294/1080|98/359|| GT:DP:RO:QR:AO:QA:GL 1/1:75:0:0:75:2721:-245.092,-22.5773,0
53 MT_H37RV_BRD_V5 4254477 . T C 225.007 . DP=30;VDB=0.000342098;SGB=-0.693021;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,10,17;MQ=60;FQ=-999 GT:PL 1:255,0 49 Chromosome 3587446 . G A 1562.41 . AB=0;AO=49;DP=49;QA=1766;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3210c|GENE_Rv3210c|transcript|TRANSCRIPT_Rv3210c|protein_coding|1/1|c.94C>T|p.Leu32Leu|94/696|94/696|32/231|| GT:DP:RO:QR:AO:QA:GL 1/1:49:0:0:49:1766:-159.195,-14.7505,0
50 Chromosome 4254431 . G A 1391.26 . AB=0;AO=46;DP=46;QA=1617;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3799c|GENE_Rv3799c|transcript|TRANSCRIPT_Rv3799c|protein_coding|1/1|c.1518C>T|p.Asp506Asp|1518/1569|1518/1569|506/522|| GT:DP:RO:QR:AO:QA:GL 1/1:46:0:0:46:1617:-145.801,-13.8474,0
51 Chromosome 4254477 . T C 760.909 . AB=0;AO=26;DP=26;QA=933;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3799c|GENE_Rv3799c|transcript|TRANSCRIPT_Rv3799c|protein_coding|1/1|c.1472A>G|p.His491Arg|1472/1569|1472/1569|491/522|| GT:DP:RO:QR:AO:QA:GL 1/1:26:0:0:26:933:-84.2834,-7.82678,0