Mercurial > repos > iuc > ensembl_vep

annotate test-data/output_test2.vcf @ 4:fdbd97ff825e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit d55061b50f807285fc8635de681992a61621447e
author iuc
date Wed, 23 Aug 2023 16:15:21 +0000
parents b43df0ce6c87
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7303183cdb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2db33cd5bcf5e2d7e3a43f11855c4cfc3b1b9f56
iuc
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diff changeset
1 ##fileformat=VCFv4.1
7303183cdb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2db33cd5bcf5e2d7e3a43f11855c4cfc3b1b9f56
iuc
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diff changeset
2 ##contig=<ID=21,assembly=GCF_000001405.26,length=46709983>
7303183cdb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2db33cd5bcf5e2d7e3a43f11855c4cfc3b1b9f56
iuc
parents:
diff changeset
3 ##contig=<ID=22,assembly=GCF_000001405.26,length=50818468>
7303183cdb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2db33cd5bcf5e2d7e3a43f11855c4cfc3b1b9f56
iuc
parents:
diff changeset
4 ##ALT=<ID=CNV,Description="Copy Number Polymorphism">
7303183cdb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2db33cd5bcf5e2d7e3a43f11855c4cfc3b1b9f56
iuc
parents:
diff changeset
5 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
7303183cdb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2db33cd5bcf5e2d7e3a43f11855c4cfc3b1b9f56
iuc
parents:
diff changeset
6 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
7303183cdb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2db33cd5bcf5e2d7e3a43f11855c4cfc3b1b9f56
iuc
parents:
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7 ##INFO=<ID=CSQ,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|SOURCE|custom_annotation.gtf.gz">
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b43df0ce6c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2d42622b1aafec3492a8e42a15c52e4b96f55b8b
iuc
parents: 0
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8 ##INFO=<ID=custom_annotation.gtf.gz,Number=.,Type=String,Description="custom_annotation.gtf.gz">
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7303183cdb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2db33cd5bcf5e2d7e3a43f11855c4cfc3b1b9f56
iuc
parents:
diff changeset
9 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096
7303183cdb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2db33cd5bcf5e2d7e3a43f11855c4cfc3b1b9f56
iuc
parents:
diff changeset
10 21 5733 rs142513484 C T . . CSQ=T|3_prime_UTR_variant|MODIFIER|MRPL39|ENSG00000154719|Transcript|ENST00000307301|protein_coding|3/3||||159|||||||-1||||custom_annotation.gtf.gz|,T|missense_variant|MODERATE|MRPL39|ENSG00000154719|Transcript|ENST00000352957|protein_coding|2/2||||70|70|24|A/T|Gca/Aca|||-1||||custom_annotation.gtf.gz|,T|upstream_gene_variant|MODIFIER|AP000223.42|ENSG00000260583|Transcript|ENST00000567517|antisense|||||||||||2407|-1||||custom_annotation.gtf.gz| GT 0|0