Mercurial > repos > iuc > cutesv

annotate test-data/output.vcf @ 0:c0f8fe52948e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
author iuc
date Thu, 24 Sep 2020 15:11:57 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
1 ##fileformat=VCFv4.2
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
2 ##source=cuteSV-1.0.8
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
3 ##fileDate=2020-09-24 12:14:05 4-CEST
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
4 ##contig=<ID=chrM,length=16571>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
5 ##ALT=<ID=INS,Description="Insertion of novel sequence relative to the reference">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
6 ##ALT=<ID=DEL,Description="Deletion relative to the reference">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
7 ##ALT=<ID=DUP,Description="Region of elevated copy number relative to the reference">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
8 ##ALT=<ID=INV,Description="Inversion of reference sequence">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
9 ##ALT=<ID=BND,Description="Breakend of translocation">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
10 ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variant">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
11 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variant">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
12 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
13 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
14 ##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
15 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
16 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
17 ##INFO=<ID=CILEN,Number=2,Type=Integer,Description="Confidence interval around inserted/deleted material between breakends">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
18 ##INFO=<ID=RE,Number=1,Type=Integer,Description="Number of read support this record">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
19 ##INFO=<ID=STRAND,Number=A,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
20 ##INFO=<ID=RNAMES,Number=.,Type=String,Description="Supporting read names of SVs (comma separated)">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
21 ##FILTER=<ID=q5,Description="Quality below 5">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
22 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
23 ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# High-quality reference reads">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
24 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# High-quality variant reads">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
25 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="# Phred-scaled genotype likelihoods rounded to the closest integer">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
26 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="# Genotype quality">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
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"
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
28 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample