Mercurial > repos > iuc > vcf2maf
annotate test-data/input_test1.vcf @ 0:2973994fecd6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit 30046d5e0df4d80ac687edd03cf44b2afaa04550
| author | iuc |
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| date | Tue, 28 Jun 2022 21:07:04 +0000 |
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| rev | line source |
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2973994fecd6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit 30046d5e0df4d80ac687edd03cf44b2afaa04550
iuc
parents:
diff
changeset
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1 ##fileformat=VCFv4.1 |
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2973994fecd6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit 30046d5e0df4d80ac687edd03cf44b2afaa04550
iuc
parents:
diff
changeset
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2 ##contig=<ID=21,assembly=GCF_000001405.26,length=46709983> |
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2973994fecd6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit 30046d5e0df4d80ac687edd03cf44b2afaa04550
iuc
parents:
diff
changeset
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3 ##contig=<ID=22,assembly=GCF_000001405.26,length=50818468> |
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2973994fecd6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit 30046d5e0df4d80ac687edd03cf44b2afaa04550
iuc
parents:
diff
changeset
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4 ##ALT=<ID=CNV,Description="Copy Number Polymorphism"> |
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2973994fecd6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit 30046d5e0df4d80ac687edd03cf44b2afaa04550
iuc
parents:
diff
changeset
|
5 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> |
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2973994fecd6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit 30046d5e0df4d80ac687edd03cf44b2afaa04550
iuc
parents:
diff
changeset
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6 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> |
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2973994fecd6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit 30046d5e0df4d80ac687edd03cf44b2afaa04550
iuc
parents:
diff
changeset
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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 |
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2973994fecd6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit 30046d5e0df4d80ac687edd03cf44b2afaa04550
iuc
parents:
diff
changeset
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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"> |
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2973994fecd6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit 30046d5e0df4d80ac687edd03cf44b2afaa04550
iuc
parents:
diff
changeset
|
9 ##INFO=<ID=custom_annotation.gtf.gz,Number=.,Type=String,Description="custom_annotation.gtf.gz (overlap)"> |
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2973994fecd6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit 30046d5e0df4d80ac687edd03cf44b2afaa04550
iuc
parents:
diff
changeset
|
10 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 |
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2973994fecd6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit 30046d5e0df4d80ac687edd03cf44b2afaa04550
iuc
parents:
diff
changeset
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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 |