Mercurial > repos > jjohnson > ensembl_variant_report

annotate test-data/GRCh38_X400k_ANN.vcf @ 2:f87fe6bc48f4 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 6b6e5c13531bf909c4c70b7f8f9e28b4206d9068-dirty
author jjohnson
date Mon, 18 Mar 2019 21:43:34 -0400
parents 9f4ea174ce3d
children
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9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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1 ##fileformat=VCFv4.2
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2 ##FILTER=<ID=PASS,Description="All filters passed">
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3 ##samtoolsVersion=1.2+htslib-1.2.1
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4 ##samtoolsCommand=samtools mpileup -f /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/seq/GRCh38_canon.fa --BCF --output-tags DP,DPR,DV,DP4,INFO/DPR,SP --output /panfs/roc/galaxy/GALAXYP/files/000/144/dataset_144978.dat localbam_0.bam
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5 ##reference=file:///panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/seq/GRCh38_canon.fa
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6 ##contig=<ID=1,length=248956422>
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7 ##contig=<ID=2,length=242193529>
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8 ##contig=<ID=3,length=198295559>
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9 ##contig=<ID=4,length=190214555>
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10 ##contig=<ID=5,length=181538259>
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11 ##contig=<ID=6,length=170805979>
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12 ##contig=<ID=7,length=159345973>
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13 ##contig=<ID=8,length=145138636>
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14 ##contig=<ID=9,length=138394717>
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15 ##contig=<ID=10,length=133797422>
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16 ##contig=<ID=11,length=135086622>
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17 ##contig=<ID=12,length=133275309>
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18 ##contig=<ID=13,length=114364328>
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19 ##contig=<ID=14,length=107043718>
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20 ##contig=<ID=15,length=101991189>
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21 ##contig=<ID=16,length=90338345>
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22 ##contig=<ID=17,length=83257441>
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23 ##contig=<ID=18,length=80373285>
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24 ##contig=<ID=19,length=58617616>
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25 ##contig=<ID=20,length=64444167>
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26 ##contig=<ID=21,length=46709983>
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27 ##contig=<ID=22,length=50818468>
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28 ##contig=<ID=X,length=156040895>
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29 ##contig=<ID=Y,length=57227415>
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30 ##contig=<ID=MT,length=16569>
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31 ##ALT=<ID=X,Description="Represents allele(s) other than observed.">
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32 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
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33 ##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
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34 ##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
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35 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
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36 ##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">
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37 ##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
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38 ##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
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39 ##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
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40 ##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
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41 ##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
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42 ##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
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43 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
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44 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
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45 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
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46 ##FORMAT=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele">
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47 ##INFO=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele">
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48 ##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases">
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49 ##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
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50 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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51 ##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
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52 ##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
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53 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
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54 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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55 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
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56 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
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57 ##bcftools_callVersion=1.3+htslib-1.3
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58 ##bcftools_callCommand=call -m --variants-only --output-type b --threads 1 input.bcf
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59 ##bcftools_viewVersion=1.3+htslib-1.3
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60 ##bcftools_viewCommand=view --exclude 'DP < 5 || DPR[1] < 3 || MIN(DV/DP)<0.33' --targets ^Mt --output-type v --threads 1 input.bcf
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61 ##bcftools_viewCommand=view --exclude 'DP < 5 || DPR[1] < 3 || MIN(DV/DP)<0.33' --targets X --output-type v --threads 1 input.vcf.gz
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62 ##bcftools_viewCommand=view --exclude 'DP < 5 || DPR[1] < 3 || MIN(DV/DP)<0.33' --regions X:1-400000 --output-type v --threads 1 input.vcf.gz
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63 ##SnpEffVersion="4.1l (build 2015-10-03), by Pablo Cingolani"
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64 ##SnpEffCmd="SnpEff -i vcf -o vcf -no-downstream -no-intergenic -no-intron -no-upstream -no-utr -no CDS -no CHROMOSOME_LARGE_DELETION -no CODON_CHANGE -no CODON_INSERTION -no CODON_CHANGE_PLUS_CODON_INSERTION -no CODON_DELETION -no CODON_CHANGE_PLUS_CODON_DELETION -no DOWNSTREAM -no EXON -no EXON_DELETED -no GENE -no INTERGENIC -no INTERGENIC_CONSERVED -no INTRAGENIC -no INTRON -no INTRON_CONSERVED -no MICRO_RNA -no NON_SYNONYMOUS_START -no NON_SYNONYMOUS_STOP -no RARE_AMINO_ACID -no SPLICE_SITE_ACCEPTOR -no SPLICE_SITE_DONOR -no SPLICE_SITE_REGION -no SPLICE_SITE_BRANCH -no SPLICE_SITE_BRANCH_U12 -no STOP_LOST -no START_GAINED -no START_LOST -no STOP_GAINED -no SYNONYMOUS_CODING -no SYNONYMOUS_START -no SYNONYMOUS_STOP -no REGULATION -no UPSTREAM -no UTR_3_PRIME -no UTR_3_DELETED -no UTR_5_PRIME -no UTR_5_DELETED -no NEXT_PROT -stats /panfs/roc/galaxy/GALAXYP/files/000/148/dataset_148016.dat GRCh38.78 /panfs/roc/galaxy/GALAXYP/files/000/148/dataset_148008.dat "
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65 ##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' ">
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66 ##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' ">
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67 ##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' ">
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68 ##SnpSiftVersion="SnpSift 4.1l (build 2015-10-03), by Pablo Cingolani"
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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69 ##SnpSiftCmd="SnpSift filter -f /panfs/roc/galaxy/GALAXYP/files/000/148/dataset_148015.dat -e /panfs/roc/galaxy/GALAXYP/job_working_directory/000/126/126606/tmpTp3aAM"
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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70 ##FILTER=<ID=SnpSift,Description="SnpSift 4.1l (build 2015-10-03), by Pablo Cingolani, Expression used: ( ANN[*].EFFECT has 'missense_variant' | ANN[*].EFFECT has 'frameshift_variant')">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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71 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT localbam_0.bam
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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72 X 284201 . T C 219.0 . DP=693;VDB=0.999766;SGB=-0.693147;RPB=1;MQB=1;MQSB=0.382033;BQB=1;MQ0F=0.001443;DPR=1,598;AC=2;AN=2;DP4=1,0,425,173;MQ=17;ANN=C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381657|ensembl_havana|2/7|n.14T>C|p.Val5Ala|528/5507|14/-1|5/-1||,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000399012|havana|3/8|n.14T>C|p.Val5Ala|311/5287|14/-1|5/-1||,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000430923|havana|2/5|n.14T>C|p.Val5Ala|77/587|14/-1|5/-1||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000445062|havana|3/4|n.14T>C|p.Val5Ala|305/555|14/-1|5/-1||WARNING_TRANSCRIPT_NO_STOP_CODON,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000429181|havana|3/4|n.14T>C|p.Val5Ala|301/469|14/-1|5/-1||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381663|ensembl|2/8|n.14T>C|p.Val5Ala|258/1863|14/-1|5/-1||,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000443019|havana|2/3|n.14T>C|p.Val5Ala|74/284|14/-1|5/-1||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000415337|havana|2/5|n.14T>C|p.Val5Ala|59/579|14/-1|5/-1||WARNING_TRANSCRIPT_NO_STOP_CODON,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000447472|havana|2/5|n.14T>C|p.Val5Ala|77/587|14/-1|5/-1||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000448477|havana|1/3|n.14T>C|p.Val5Ala|468/828|14/-1|5/-1||WARNING_TRANSCRIPT_INCOMPLETE GT:PL:DP:DV:SP:DP4:DPR 1/1:246,255,0:599:598:0:1,0,425,173:1,598
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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73 X 288851 . G GC 30.4966 . DP=21;VDB=0.0115453;SGB=-0.670168;RPB=0.597928;MQB=1;BQB=0.968368;MQ0F=0;DPR=3,10;ICB=1;HOB=0.5;AC=1;AN=2;DP4=3,0,10,0;MQ=20;ANN=GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000381657|ensembl_havana|3/7|n.246_247insC|p.Lys83fs|761/5507|247/-1|83/-1||,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000399012|havana|4/8|n.246_247insC|p.Lys83fs|544/5287|247/-1|83/-1||,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000430923|havana|3/5|n.246_247insC|p.Lys83fs|310/587|247/-1|83/-1||WARNING_TRANSCRIPT_INCOMPLETE,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000445062|havana|4/4|n.246_247insC|p.Lys83fs|538/555|247/-1|83/-1||WARNING_TRANSCRIPT_NO_STOP_CODON,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000381663|ensembl|3/8|n.246_247insC|p.Lys83fs|491/1863|247/-1|83/-1||,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000415337|havana|3/5|n.246_247insC|p.Lys83fs|292/579|247/-1|83/-1||WARNING_TRANSCRIPT_NO_STOP_CODON,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000447472|havana|3/5|n.246_247insC|p.Lys83fs|310/587|247/-1|83/-1||WARNING_TRANSCRIPT_INCOMPLETE,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000448477|havana|2/3|n.246_247insC|p.Lys83fs|701/828|247/-1|83/-1||WARNING_TRANSCRIPT_INCOMPLETE GT:PL:DP:DV:SP:DP4:DPR 0/1:64,0,15:13:10:0:3,0,10,0:3,10
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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74 X 290695 . C G 114.0 . DP=910;VDB=0.336517;SGB=-0.693147;RPB=0.479982;MQB=0.997299;MQSB=0.999049;BQB=0.555736;MQ0F=0.010989;DPR=130,681;AC=2;AN=2;DP4=72,58,392,289;MQ=18;ANN=G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381657|ensembl_havana|4/7|n.312C>G|p.Asp104Glu|826/5507|312/-1|104/-1||,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000399012|havana|5/8|n.312C>G|p.Asp104Glu|609/5287|312/-1|104/-1||,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000484611|havana|4/5|n.404C>G|p.Thr135Ser|404/540|404/-1|135/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000430923|havana|4/5|n.312C>G|p.Asp104Glu|375/587|312/-1|104/-1||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381663|ensembl|4/8|n.312C>G|p.Asp104Glu|556/1863|312/-1|104/-1||,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000415337|havana|4/5|n.312C>G|p.Asp104Glu|357/579|312/-1|104/-1||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000447472|havana|4/5|n.312C>G|p.Asp104Glu|375/587|312/-1|104/-1||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000448477|havana|3/3|n.312C>G|p.Asp104Glu|766/828|312/-1|104/-1||WARNING_TRANSCRIPT_INCOMPLETE GT:PL:DP:DV:SP:DP4:DPR 1/1:141,210,0:811:681:2:72,58,392,289:130,681
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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75 X 299221 . G C 77.0 . DP=18;VDB=0.00122481;SGB=-0.683931;RPB=0.169694;MQB=1;MQSB=1;BQB=0.560355;MQ0F=0;DPR=3,13;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,2,9,4;MQ=20;ANN=C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381657|ensembl_havana|7/7|n.858G>C|p.Glu286Asp|1372/5507|858/-1|286/-1||,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000399012|havana|8/8|n.858G>C|p.Glu286Asp|1155/5287|858/-1|286/-1||,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381663|ensembl|7/8|n.858G>C|p.Glu286Asp|1102/1863|858/-1|286/-1|| GT:PL:DP:DV:SP:DP4:DPR 0/1:110,0,10:16:13:3:1,2,9,4:3,13
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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76 X 307850 . G C 40.3947 . DP=24;VDB=0.351291;SGB=-0.651104;RPB=0.511891;MQB=1;MQSB=1;BQB=0.720273;MQ0F=0;DPR=7,8;ICB=1;HOB=0.5;AC=1;AN=2;DP4=5,2,6,2;MQ=20;ANN=C|missense_variant|MODERATE|GTPBP6|ENSG00000178605|transcript|ENST00000485332|havana|2/4|n.1076C>G|p.Pro359Arg|1076/2016|1076/-1|359/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|missense_variant|MODERATE|GTPBP6|ENSG00000178605|transcript|ENST00000326153|ensembl_havana|8/10|n.1156C>G|p.His386Asp|1188/1907|1156/-1|386/-1|| GT:PL:DP:DV:SP:DP4:DPR 0/1:73,0,69:15:8:0:5,2,6,2:7,8
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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77 X 311500 . C CAT 59.0 . DP=56;VDB=0.625112;SGB=-0.692562;RPB=0.999818;MQB=0.915545;MQSB=0.982508;BQB=0.929674;MQ0F=0;DPR=11,22;ICB=1;HOB=0.5;AC=1;AN=2;DP4=11,0,19,3;MQ=18;ANN=CAT|frameshift_variant|HIGH|GTPBP6|ENSG00000178605|transcript|ENST00000485332|havana|1/4|n.963_964insAT|p.Gly322fs|963/2016|963/-1|321/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,CAT|frameshift_variant|HIGH|GTPBP6|ENSG00000178605|transcript|ENST00000326153|ensembl_havana|7/10|n.1043_1044insAT|p.Asp349fs|1075/1907|1043/-1|348/-1|| GT:PL:DP:DV:SP:DP4:DPR 0/1:92,0,40:33:22:3:11,0,19,3:11,22
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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78 X 334496 . A G 30.4121 . DP=159;VDB=0.0384616;SGB=-0.693147;RPB=0.000107797;MQB=0.271035;MQSB=0.730753;BQB=0.124283;MQ0F=0.0880503;DPR=52,60;ICB=1;HOB=0.5;AC=1;AN=2;DP4=48,4,58,3;MQ=16;ANN=G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|8/8|n.5545T>C|p.Cys1849Arg|5545/5802|5545/-1|1849/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|5/5|n.829T>C|p.Cys277Arg|829/1090|829/-1|277/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:PL:DP:DV:SP:DP4:DPR 0/1:63,0,72:113:61:2:48,4,58,3:52,60
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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79 X 338625 . G A 74.0 . DP=308;VDB=6.22534e-11;SGB=-0.693147;RPB=0.0585974;MQB=0.956346;MQSB=0.973687;BQB=0.279044;MQ0F=0.0681818;DPR=146,132;ICB=1;HOB=0.5;AC=1;AN=2;DP4=122,24,108,24;MQ=16;ANN=A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|12/13|n.1556C>T|p.Ala519Val|1575/2151|1556/-1|519/-1||,A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000468169|havana|5/5|n.701C>T|p.Ala234Val|701/713|701/-1|234/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:PL:DP:DV:SP:DP4:DPR 0/1:107,0,99:278:132:1:122,24,108,24:146,132
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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80 X 338627 . A G 190.0 . DP=301;VDB=1.9745e-09;SGB=-0.693147;MQSB=0.973119;MQ0F=0.0697674;DPR=0,271;AC=2;AN=2;DP4=0,0,229,42;MQ=16;ANN=G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|8/8|n.1414T>C|p.Cys472Arg|1414/5802|1414/-1|472/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|4/5|n.784T>C|p.Cys262Arg|784/1090|784/-1|262/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:PL:DP:DV:SP:DP4:DPR 1/1:217,255,0:271:271:0:0,0,229,42:0,271
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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81 X 338856 . A G 182.0 . DP=517;VDB=0.238596;SGB=-0.693147;RPB=0.857702;MQB=0.810962;MQSB=0.0368774;BQB=0.944745;MQ0F=0.0135397;DPR=15,390;AC=2;AN=2;DP4=7,8,244,146;MQ=16;ANN=G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000468169|havana|5/5|n.470T>C|p.Leu157Pro|470/713|470/-1|157/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:PL:DP:DV:SP:DP4:DPR 1/1:209,255,0:405:390:6:7,8,244,146:15,390
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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82 X 340856 . CTG C 107.0 . DP=17;VDB=3.781e-05;SGB=-0.676189;MQSB=0.8618;MQ0F=0;DPR=0,11;AC=2;AN=2;DP4=0,0,6,5;MQ=18;ANN=C|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|6/8|n.1118_1119delCA|p.Ala373fs|1119/5802|1118/-1|373/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|10/13|n.1258_1259delCA|p.Gln420fs|1278/2151|1258/-1|420/-1||,C|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|2/5|n.488_489delCA|p.Ala163fs|489/1090|488/-1|163/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000468169|havana|4/5|n.336_337delCA|p.Ser112fs|337/713|336/-1|112/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000484364|havana|4/4|n.639_640delCA|p.Ser213fs|640/732|639/-1|213/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:PL:DP:DV:SP:DP4:DPR 1/1:134,33,0:11:11:0:0,0,6,5:0,11
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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83 X 340928 . C CA 181.0 . DP=65;VDB=2.0017e-11;SGB=-0.693147;MQSB=0.996914;MQ0F=0;DPR=0,50;AC=2;AN=2;DP4=0,0,21,29;MQ=19;ANN=CA|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|6/8|n.1047_1048insT|p.Val350fs|1047/5802|1047/-1|349/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,CA|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|10/13|n.1187_1188insT|p.Trp396fs|1206/2151|1187/-1|396/-1||,CA|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|2/5|n.417_418insT|p.Val140fs|417/1090|417/-1|139/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,CA|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000468169|havana|4/5|n.265_266insT|p.Gly89fs|265/713|265/-1|89/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,CA|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000484364|havana|4/4|n.568_569insT|p.Gly190fs|568/732|568/-1|190/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:PL:DP:DV:SP:DP4:DPR 1/1:208,151,0:50:50:0:0,0,21,29:0,50
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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84 X 341347 . A C,G 170.0 . DP=48;VDB=0.802018;SGB=-0.693136;MQSB=0.969233;MQ0F=0;DPR=0,20,15;AC=2;AN=2;DP4=0,0,20,15;MQ=19;ANN=C|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|5/8|n.995T>G|p.Leu332Arg|995/5802|995/-1|332/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|5/8|n.995T>C|p.Leu332Pro|995/5802|995/-1|332/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|9/13|n.1135T>G|p.Trp379Gly|1154/2151|1135/-1|379/-1||,G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|9/13|n.1135T>C|p.Trp379Arg|1154/2151|1135/-1|379/-1||,C|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|1/5|n.365T>G|p.Leu122Arg|365/1090|365/-1|122/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|1/5|n.365T>C|p.Leu122Pro|365/1090|365/-1|122/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:PL:DP:DV:SP:DP4:DPR 1/1:197,105,0:35:35:0:0,0,20,15:0,20,15
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
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parents:
diff changeset
85 X 345580 . G A 41.8455 . DP=6;VDB=0.910845;SGB=-0.556411;MQSB=1;MQ0F=0;DPR=0,4;AC=2;AN=2;DP4=0,0,3,1;MQ=20;ANN=A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|7/13|n.972C>T|p.Trp324Cys|991/2151|972/-1|324/-1||WARNING_REF_DOES_NOT_MATCH_GENOME,A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000468169|havana|1/5|n.50C>T|p.Gly17Val|50/713|50/-1|17/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME,A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000484364|havana|1/4|n.47C>T|p.Gly16Val|47/732|47/-1|16/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME,A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000477636|havana|2/3|n.434C>T|p.Gly145Val|434/519|434/-1|145/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME,A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000445792|havana|8/8|n.1314C>T|p.Trp438Cys|1314/1998|1314/-1|438/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME GT:PL:DP:DV:SP:DP4:DPR 1/1:69,12,0:4:4:0:0,0,3,1:0,4