diff test-data/input.vcf @ 0:fb00426402b0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.vcf	Mon Jan 25 17:50:47 2021 +0000
@@ -0,0 +1,140 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20200728
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP,Description="Duplication">
+##ALT=<ID=INV,Description="Inversion">
+##ALT=<ID=BND,Description="Translocation">
+##ALT=<ID=INS,Description="Insertion">
+##FILTER=<ID=LowQual,Description="Poor quality and insufficient number of PEs and SRs.">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="PE confidence interval around END">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="PE confidence interval around POS">
+##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for POS2 coordinate in case of an inter-chromosomal translocation">
+##INFO=<ID=POS2,Number=1,Type=Integer,Description="Genomic position for CHR2 in case of an inter-chromosomal translocation">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
+##INFO=<ID=PE,Number=1,Type=Integer,Description="Paired-end support of the structural variant">
+##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends">
+##INFO=<ID=SRMAPQ,Number=1,Type=Integer,Description="Median mapping quality of split-reads">
+##INFO=<ID=SR,Number=1,Type=Integer,Description="Split-read support">
+##INFO=<ID=SRQ,Number=1,Type=Float,Description="Split-read consensus alignment quality">
+##INFO=<ID=CONSENSUS,Number=1,Type=String,Description="Split-read consensus sequence">
+##INFO=<ID=CE,Number=1,Type=Float,Description="Consensus sequence entropy">
+##INFO=<ID=CT,Number=1,Type=String,Description="Paired-end signature induced connection type">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Insertion length for SVTYPE=INS.">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
+##INFO=<ID=INSLEN,Number=1,Type=Integer,Description="Predicted length of the insertion">
+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Predicted microhomology length using a max. edit distance of 2">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Log10-scaled genotype likelihoods for RR,RA,AA genotypes">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Per-sample genotype filter">
+##FORMAT=<ID=RC,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the SV">
+##FORMAT=<ID=RCL,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the left control region">
+##FORMAT=<ID=RCR,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the right control region">
+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Read-depth based copy-number estimate for autosomal sites">
+##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference pairs">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant pairs">
+##FORMAT=<ID=RR,Number=1,Type=Integer,Description="# high-quality reference junction reads">
+##FORMAT=<ID=RV,Number=1,Type=Integer,Description="# high-quality variant junction reads">
+##reference=../data/v1/genome.fasta
+##contig=<ID=chr10,length=135534747>
+##contig=<ID=chr11,length=135006516>
+##contig=<ID=chr11_gl000202_random,length=40103>
+##contig=<ID=chr12,length=133851895>
+##contig=<ID=chr13,length=115169878>
+##contig=<ID=chr14,length=107349540>
+##contig=<ID=chr15,length=102531392>
+##contig=<ID=chr16,length=90354753>
+##contig=<ID=chr17_ctg5_hap1,length=1680828>
+##contig=<ID=chr17,length=81195210>
+##contig=<ID=chr17_gl000203_random,length=37498>
+##contig=<ID=chr17_gl000204_random,length=81310>
+##contig=<ID=chr17_gl000205_random,length=174588>
+##contig=<ID=chr17_gl000206_random,length=41001>
+##contig=<ID=chr18,length=78077248>
+##contig=<ID=chr18_gl000207_random,length=4262>
+##contig=<ID=chr19,length=59128983>
+##contig=<ID=chr19_gl000208_random,length=92689>
+##contig=<ID=chr19_gl000209_random,length=159169>
+##contig=<ID=chr1,length=249250621>
+##contig=<ID=chr1_gl000191_random,length=106433>
+##contig=<ID=chr1_gl000192_random,length=547496>
+##contig=<ID=chr20,length=63025520>
+##contig=<ID=chr21,length=48129895>
+##contig=<ID=chr21_gl000210_random,length=27682>
+##contig=<ID=chr22,length=51304566>
+##contig=<ID=chr2,length=243199373>
+##contig=<ID=chr3,length=198022430>
+##contig=<ID=chr4_ctg9_hap1,length=590426>
+##contig=<ID=chr4,length=191154276>
+##contig=<ID=chr4_gl000193_random,length=189789>
+##contig=<ID=chr4_gl000194_random,length=191469>
+##contig=<ID=chr5,length=180915260>
+##contig=<ID=chr6_apd_hap1,length=4622290>
+##contig=<ID=chr6_cox_hap2,length=4795371>
+##contig=<ID=chr6_dbb_hap3,length=4610396>
+##contig=<ID=chr6,length=171115067>
+##contig=<ID=chr6_mann_hap4,length=4683263>
+##contig=<ID=chr6_mcf_hap5,length=4833398>
+##contig=<ID=chr6_qbl_hap6,length=4611984>
+##contig=<ID=chr6_ssto_hap7,length=4928567>
+##contig=<ID=chr7,length=159138663>
+##contig=<ID=chr7_gl000195_random,length=182896>
+##contig=<ID=chr8,length=146364022>
+##contig=<ID=chr8_gl000196_random,length=38914>
+##contig=<ID=chr8_gl000197_random,length=37175>
+##contig=<ID=chr9,length=141213431>
+##contig=<ID=chr9_gl000198_random,length=90085>
+##contig=<ID=chr9_gl000199_random,length=169874>
+##contig=<ID=chr9_gl000200_random,length=187035>
+##contig=<ID=chr9_gl000201_random,length=36148>
+##contig=<ID=chrM,length=16571>
+##contig=<ID=chrUn_gl000211,length=166566>
+##contig=<ID=chrUn_gl000212,length=186858>
+##contig=<ID=chrUn_gl000213,length=164239>
+##contig=<ID=chrUn_gl000214,length=137718>
+##contig=<ID=chrUn_gl000215,length=172545>
+##contig=<ID=chrUn_gl000216,length=172294>
+##contig=<ID=chrUn_gl000217,length=172149>
+##contig=<ID=chrUn_gl000218,length=161147>
+##contig=<ID=chrUn_gl000219,length=179198>
+##contig=<ID=chrUn_gl000220,length=161802>
+##contig=<ID=chrUn_gl000221,length=155397>
+##contig=<ID=chrUn_gl000222,length=186861>
+##contig=<ID=chrUn_gl000223,length=180455>
+##contig=<ID=chrUn_gl000224,length=179693>
+##contig=<ID=chrUn_gl000225,length=211173>
+##contig=<ID=chrUn_gl000226,length=15008>
+##contig=<ID=chrUn_gl000227,length=128374>
+##contig=<ID=chrUn_gl000228,length=129120>
+##contig=<ID=chrUn_gl000229,length=19913>
+##contig=<ID=chrUn_gl000230,length=43691>
+##contig=<ID=chrUn_gl000231,length=27386>
+##contig=<ID=chrUn_gl000232,length=40652>
+##contig=<ID=chrUn_gl000233,length=45941>
+##contig=<ID=chrUn_gl000234,length=40531>
+##contig=<ID=chrUn_gl000235,length=34474>
+##contig=<ID=chrUn_gl000236,length=41934>
+##contig=<ID=chrUn_gl000237,length=45867>
+##contig=<ID=chrUn_gl000238,length=39939>
+##contig=<ID=chrUn_gl000239,length=33824>
+##contig=<ID=chrUn_gl000240,length=41933>
+##contig=<ID=chrUn_gl000241,length=42152>
+##contig=<ID=chrUn_gl000242,length=43523>
+##contig=<ID=chrUn_gl000243,length=43341>
+##contig=<ID=chrUn_gl000244,length=39929>
+##contig=<ID=chrUn_gl000245,length=36651>
+##contig=<ID=chrUn_gl000246,length=38154>
+##contig=<ID=chrUn_gl000247,length=36422>
+##contig=<ID=chrUn_gl000248,length=39786>
+##contig=<ID=chrUn_gl000249,length=38502>
+##contig=<ID=chrX,length=155270560>
+##contig=<ID=chrY,length=59373566>
+##INFO=<ID=RDRATIO,Number=1,Type=Float,Description="Read-depth ratio of tumor vs. normal.">
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic structural variant.">
+##bcftools_viewVersion=1.10.2+htslib-1.10.2
+##bcftools_viewCommand=view sv.bcf; Date=Mon Sep 21 22:19:50 2020
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR