diff test-data/output_test2.vcf @ 0:7303183cdb87 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2db33cd5bcf5e2d7e3a43f11855c4cfc3b1b9f56
author iuc
date Wed, 11 May 2022 13:03:38 +0000
parents
children b43df0ce6c87
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_test2.vcf	Wed May 11 13:03:38 2022 +0000
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+##fileformat=VCFv4.1
+##contig=<ID=21,assembly=GCF_000001405.26,length=46709983>
+##contig=<ID=22,assembly=GCF_000001405.26,length=50818468>
+##ALT=<ID=CNV,Description="Copy Number Polymorphism">
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##VEP="v105" time="2022-03-30 19:24:59" ensembl=105.525fbcb ensembl-io=105.2a0a40c ensembl-funcgen=105.660df8f ensembl-variation=105.ac8178e
+##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">
+##INFO=<ID=custom_annotation.gtf.gz,Number=.,Type=String,Description="custom_annotation.gtf.gz (overlap)">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00096
+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