Mercurial > repos > iuc > cutesv
comparison test-data/output.vcf @ 0:c0f8fe52948e draft default tip
"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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-1:000000000000 | 0:c0f8fe52948e |
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1 ##fileformat=VCFv4.2 | |
2 ##source=cuteSV-1.0.8 | |
3 ##fileDate=2020-09-24 12:14:05 4-CEST | |
4 ##contig=<ID=chrM,length=16571> | |
5 ##ALT=<ID=INS,Description="Insertion of novel sequence relative to the reference"> | |
6 ##ALT=<ID=DEL,Description="Deletion relative to the reference"> | |
7 ##ALT=<ID=DUP,Description="Region of elevated copy number relative to the reference"> | |
8 ##ALT=<ID=INV,Description="Inversion of reference sequence"> | |
9 ##ALT=<ID=BND,Description="Breakend of translocation"> | |
10 ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variant"> | |
11 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variant"> | |
12 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> | |
13 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles"> | |
14 ##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation"> | |
15 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> | |
16 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> | |
17 ##INFO=<ID=CILEN,Number=2,Type=Integer,Description="Confidence interval around inserted/deleted material between breakends"> | |
18 ##INFO=<ID=RE,Number=1,Type=Integer,Description="Number of read support this record"> | |
19 ##INFO=<ID=STRAND,Number=A,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> | |
20 ##INFO=<ID=RNAMES,Number=.,Type=String,Description="Supporting read names of SVs (comma separated)"> | |
21 ##FILTER=<ID=q5,Description="Quality below 5"> | |
22 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
23 ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# High-quality reference reads"> | |
24 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# High-quality variant reads"> | |
25 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="# Phred-scaled genotype likelihoods rounded to the closest integer"> | |
26 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="# Genotype quality"> | |
27 ##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" | |
28 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample |