Mercurial > repos > iuc > ensembl_vep

comparison test-data/output_test2.vcf @ 2:b43df0ce6c87 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2d42622b1aafec3492a8e42a15c52e4b96f55b8b
author iuc
date Wed, 26 Oct 2022 10:02:51 +0000
parents 7303183cdb87
children
comparison
equal deleted inserted replaced
1:27fd1c1f00a8 2:b43df0ce6c87
2 ##contig=<ID=21,assembly=GCF_000001405.26,length=46709983> 2 ##contig=<ID=21,assembly=GCF_000001405.26,length=46709983>
3 ##contig=<ID=22,assembly=GCF_000001405.26,length=50818468> 3 ##contig=<ID=22,assembly=GCF_000001405.26,length=50818468>
4 ##ALT=<ID=CNV,Description="Copy Number Polymorphism"> 4 ##ALT=<ID=CNV,Description="Copy Number Polymorphism">
5 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> 5 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
6 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> 6 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
7 ##VEP="v105" time="2022-03-30 19:24:59" ensembl=105.525fbcb ensembl-io=105.2a0a40c ensembl-funcgen=105.660df8f ensembl-variation=105.ac8178e
8 ##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"> 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">
9 ##INFO=<ID=custom_annotation.gtf.gz,Number=.,Type=String,Description="custom_annotation.gtf.gz (overlap)"> 8 ##INFO=<ID=custom_annotation.gtf.gz,Number=.,Type=String,Description="custom_annotation.gtf.gz">
10 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 9 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096
11 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 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