Mercurial > repos > iuc > bcftools_plugin_missing2ref

annotate test-data/plugin2.vcf @ 21:cb7928fcd126 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 868f4386992de55d25da197660a43a913a09c8df
author iuc
date Wed, 14 Aug 2024 16:44:58 +0000
parents 4ed46189d6c6
children
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4ed46189d6c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
iuc
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diff changeset
1 ##fileformat=VCFv4.2
4ed46189d6c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
iuc
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2 ##FILTER=<ID=PASS,Description="All filters passed">
4ed46189d6c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
iuc
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3 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype code">
4ed46189d6c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
iuc
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4 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
4ed46189d6c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
iuc
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5 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
4ed46189d6c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
iuc
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6 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
4ed46189d6c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
iuc
parents:
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7 ##FORMAT=<ID=ADF,Number=R,Type=Integer,Description="Read depth for each allele on the forward strand">
4ed46189d6c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
iuc
parents:
diff changeset
8 ##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Read depth for each allele on the reverse strand">
4ed46189d6c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
iuc
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9 ##INFO=<ID=ANN,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|SIFT|PolyPhen|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|CLIN_SIG|SOMATIC|PHENO|CAROL|Condel">
4ed46189d6c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
iuc
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10 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
4ed46189d6c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
iuc
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11 chr12 247923 . A G . PASS ANN=G|missense_variant|MODERATE|IQSEC3|ENSG00000120645|Transcript|ENST00000326261|protein_coding|4/15||||1394|1394|465|D/G|gAt/gGt|rs75677829||1||HGNC|29193|tolerated(0.23)|benign(0.015)|0.08|0.2314|0.05139|0.1233|0.01977|0.09129|0.08025|0.07976|0.07557||||Neutral(0.763)|neutral(0.042),G|missense_variant|MODERATE|IQSEC3|ENSG00000120645|Transcript|ENST00000382841|protein_coding|3/13||||897|485|162|D/G|gAt/gGt|rs75677829||1||HGNC|29193|tolerated_low_confidence(0.32)|benign(0.036)|0.08|0.2314|0.05139|0.1233|0.01977|0.09129|0.08025|0.07976|0.07557||||Neutral(0.659)|neutral(0.026),G|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-598F7.4|ENSG00000249695|Transcript|ENST00000505893|antisense||7/9||||||||rs75677829||-1||Clone_based_vega_gene||||0.08|0.2314|0.05139|0.1233|0.01977|0.09129|0.08025|0.07976|0.07557|||||,G|downstream_gene_variant|MODIFIER|RP11-598F7.4|ENSG00000249695|Transcript|ENST00000508953|antisense||||||||||rs75677829|777|-1||Clone_based_vega_gene||||0.08|0.2314|0.05139|0.1233|0.01977|0.09129|0.08025|0.07976|0.07557|||||,G|missense_variant|MODERATE|IQSEC3|ENSG00000120645|Transcript|ENST00000538872|protein_coding|4/14||||1512|1394|465|D/G|gAt/gGt|rs75677829||1||HGNC|29193|tolerated(0.23)|benign(0.015)|0.08|0.2314|0.05139|0.1233|0.01977|0.09129|0.08025|0.07976|0.07557||||Neutral(0.763)|neutral(0.042) GT:GQ:DP:AD:ADF:ADR 0/1:.:14:8,6:7,6:1,0 0/1:.:41:12,29:10,25:2,4
4ed46189d6c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
iuc
parents:
diff changeset
12 chr12 284058 . T C . PASS ANN=C|synonymous_variant|LOW|IQSEC3|ENSG00000120645|Transcript|ENST00000326261|protein_coding|14/15||||3408|3408|1136|G|ggT/ggC|rs216230&COSV58289061||1||HGNC|29193|||0.9443|0.9477|0.967|0.9298|0.8657|0.944|0.9597|0.9377|0.9158||0&1|0&1||,C|downstream_gene_variant|MODIFIER|IQSEC3|ENSG00000120645|Transcript|ENST00000382841|protein_coding||||||||||rs216230&COSV58289061|3562|1||HGNC|29193|||0.9443|0.9477|0.967|0.9298|0.8657|0.944|0.9597|0.9377|0.9158||0&1|0&1||,C|non_coding_transcript_exon_variant|MODIFIER|IQSEC3|ENSG00000120645|Transcript|ENST00000537151|processed_transcript|3/4||||378|||||rs216230&COSV58289061||1||HGNC|29193|||0.9443|0.9477|0.967|0.9298|0.8657|0.944|0.9597|0.9377|0.9158||0&1|0&1||,C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-598F7.6|ENSG00000256540|Transcript|ENST00000537295|lincRNA||1/2||||||||rs216230&COSV58289061||-1||Clone_based_vega_gene||||0.9443|0.9477|0.967|0.9298|0.8657|0.944|0.9597|0.9377|0.9158||0&1|0&1||,C|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-598F7.6|ENSG00000256540|Transcript|ENST00000537961|lincRNA||1/1||||||||rs216230&COSV58289061||-1||Clone_based_vega_gene||||0.9443|0.9477|0.967|0.9298|0.8657|0.944|0.9597|0.9377|0.9158||0&1|0&1||,C|synonymous_variant|LOW|IQSEC3|ENSG00000120645|Transcript|ENST00000538872|protein_coding|14/14||||3526|3408|1136|G|ggT/ggC|rs216230&COSV58289061||1||HGNC|29193|||0.9443|0.9477|0.967|0.9298|0.8657|0.944|0.9597|0.9377|0.9158||0&1|0&1||,C|downstream_gene_variant|MODIFIER|IQSEC3|ENSG00000120645|Transcript|ENST00000540907|retained_intron||||||||||rs216230&COSV58289061|3426|1||HGNC|29193|||0.9443|0.9477|0.967|0.9298|0.8657|0.944|0.9597|0.9377|0.9158||0&1|0&1||,C|upstream_gene_variant|MODIFIER|IQSEC3|ENSG00000120645|Transcript|ENST00000544511|processed_transcript||||||||||rs216230&COSV58289061|1590|1||HGNC|29193|||0.9443|0.9477|0.967|0.9298|0.8657|0.944|0.9597|0.9377|0.9158||0&1|0&1|| GT:GQ:DP:AD:ADF:ADR 1/1:.:13:0,13:0,5:0,8 1/1:.:48:0,48:0,14:0,34
4ed46189d6c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
iuc
parents:
diff changeset
13 chr12 285027 . C A . PASS ANN=A|3_prime_UTR_variant|MODIFIER|IQSEC3|ENSG00000120645|Transcript|ENST00000326261|protein_coding|14/15||||4377|||||rs7960096||1||HGNC|29193||||||||||||||||,A|downstream_gene_variant|MODIFIER|IQSEC3|ENSG00000120645|Transcript|ENST00000382841|protein_coding||||||||||rs7960096|4531|1||HGNC|29193||||||||||||||||,A|downstream_gene_variant|MODIFIER|IQSEC3|ENSG00000120645|Transcript|ENST00000537151|processed_transcript||||||||||rs7960096|502|1||HGNC|29193||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-598F7.6|ENSG00000256540|Transcript|ENST00000537295|lincRNA||1/2||||||||rs7960096||-1||Clone_based_vega_gene|||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-598F7.6|ENSG00000256540|Transcript|ENST00000537961|lincRNA||1/1||||||||rs7960096||-1||Clone_based_vega_gene|||||||||||||||||,A|3_prime_UTR_variant|MODIFIER|IQSEC3|ENSG00000120645|Transcript|ENST00000538872|protein_coding|14/14||||4495|||||rs7960096||1||HGNC|29193||||||||||||||||,A|downstream_gene_variant|MODIFIER|IQSEC3|ENSG00000120645|Transcript|ENST00000540907|retained_intron||||||||||rs7960096|4395|1||HGNC|29193||||||||||||||||,A|upstream_gene_variant|MODIFIER|IQSEC3|ENSG00000120645|Transcript|ENST00000544511|processed_transcript||||||||||rs7960096|621|1||HGNC|29193|||||||||||||||| GT:GQ:DP:AD:ADF:ADR 0/1:.:25:15,10:10,7:5,3 0/1:.:19:8,11:3,8:5,3