Mercurial > repos > iuc > cutesv
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
author | iuc |
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date | Thu, 24 Sep 2020 15:11:57 +0000 |
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##fileformat=VCFv4.2 ##source=cuteSV-1.0.8 ##fileDate=2020-09-24 12:14:05 4-CEST ##contig=<ID=chrM,length=16571> ##ALT=<ID=INS,Description="Insertion of novel sequence relative to the reference"> ##ALT=<ID=DEL,Description="Deletion relative to the reference"> ##ALT=<ID=DUP,Description="Region of elevated copy number relative to the reference"> ##ALT=<ID=INV,Description="Inversion of reference sequence"> ##ALT=<ID=BND,Description="Breakend of translocation"> ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variant"> ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variant"> ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles"> ##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation"> ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> ##INFO=<ID=CILEN,Number=2,Type=Integer,Description="Confidence interval around inserted/deleted material between breakends"> ##INFO=<ID=RE,Number=1,Type=Integer,Description="Number of read support this record"> ##INFO=<ID=STRAND,Number=A,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> ##INFO=<ID=RNAMES,Number=.,Type=String,Description="Supporting read names of SVs (comma separated)"> ##FILTER=<ID=q5,Description="Quality below 5"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# High-quality reference reads"> ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# High-quality variant reads"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="# Phred-scaled genotype likelihoods rounded to the closest integer"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="# Genotype quality"> ##CommandLine="cuteSV ./sample.bam ./genome.fa ./output.vcf ./ --threads 1 --batches 10000000 --sample Sample --max_split_parts 7 --min_mapq 20 --min_read_len 500 --merge_del_threshold 0 --merge_ins_threshold 100 --min_support 10 --min_size 30 --max_size 100000 --gt_round 500 --max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 200 --diff_ratio_merging_DEL 0.5 --max_cluster_bias_INV 500 --max_cluster_bias_DUP 500 --max_cluster_bias_TRA 50 --diff_ratio_filtering_TRA 0.6" #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample