Mercurial > repos > iuc > sniffles
annotate test-data/expected_outcome6.vcf @ 4:43fffeed243f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 03fbb13717809f9198ab113192d241599705ef7b
author | iuc |
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date | Sun, 29 Sep 2024 10:23:36 +0000 |
parents | 09f5c6f3088a |
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rev | line source |
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3
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
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0
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1 ##fileformat=VCFv4.2 |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
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0
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2 ##source=Sniffles2_2.4 |
4
43fffeed243f
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 03fbb13717809f9198ab113192d241599705ef7b
iuc
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3 ##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/13/outputs/dataset_93c07e69-9ce4-4394-84c8-8a51cb2e2c89.dat --allow-overwrite --reference reference.fa --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5" |
43fffeed243f
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 03fbb13717809f9198ab113192d241599705ef7b
iuc
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3
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4 ##fileDate="2024/09/28 23:21:51" |
0
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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5 ##contig=<ID=1,length=249250621> |
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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6 ##contig=<ID=2,length=243199373> |
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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81 ##contig=<ID=GL000195.1,length=182896> |
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
diff
changeset
|
82 ##contig=<ID=GL000212.1,length=186858> |
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
diff
changeset
|
83 ##contig=<ID=GL000222.1,length=186861> |
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
diff
changeset
|
84 ##contig=<ID=GL000200.1,length=187035> |
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
diff
changeset
|
85 ##contig=<ID=GL000193.1,length=189789> |
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
diff
changeset
|
86 ##contig=<ID=GL000194.1,length=191469> |
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
diff
changeset
|
87 ##contig=<ID=GL000225.1,length=211173> |
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
diff
changeset
|
88 ##contig=<ID=GL000192.1,length=547496> |
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
diff
changeset
|
89 ##contig=<ID=NC_007605,length=171823> |
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
diff
changeset
|
90 ##contig=<ID=hs37d5,length=35477943> |
3
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
91 ##ALT=<ID=INS,Description="Insertion"> |
0
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
diff
changeset
|
92 ##ALT=<ID=DEL,Description="Deletion"> |
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
diff
changeset
|
93 ##ALT=<ID=DUP,Description="Duplication"> |
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
diff
changeset
|
94 ##ALT=<ID=INV,Description="Inversion"> |
3
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
95 ##ALT=<ID=BND,Description="Breakend; Translocation"> |
0
93c4b04a0769
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
parents:
diff
changeset
|
96 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> |
3
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
97 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
98 ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="Number of reference reads"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
99 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of variant reads"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
100 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase-block, zero if none or not phased"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
101 ##FORMAT=<ID=ID,Number=1,Type=String,Description="Individual sample SV ID for multi-sample output"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
102 ##FILTER=<ID=PASS,Description="All filters passed"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
103 ##FILTER=<ID=GT,Description="Genotype filter"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
104 ##FILTER=<ID=SUPPORT_MIN,Description="Minimum read support filter"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
105 ##FILTER=<ID=STDEV_POS,Description="SV Breakpoint standard deviation filter"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
106 ##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
107 ##FILTER=<ID=COV_MIN,Description="Minimum coverage filter"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
108 ##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
109 ##FILTER=<ID=COV_CHANGE,Description="Coverage change filter"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
110 ##FILTER=<ID=COV_CHANGE_INS,Description="Coverage change filter for INS"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
111 ##FILTER=<ID=COV_CHANGE_FRAC_US,Description="Coverage fractional change filter: upstream-start"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
112 ##FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
113 ##FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
114 ##FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
115 ##FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
116 ##FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
117 ##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
118 ##FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
119 ##FILTER=<ID=STRAND,Description="Strand support filter for germline SVs"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
120 ##FILTER=<ID=STRAND_MOSAIC,Description="Strand support filter for mosaic SVs"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
121 ##FILTER=<ID=SVLEN_MIN,Description="SV length filter"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
122 ##FILTER=<ID=SVLEN_MIN_MOSAIC,Description="SV length filter for mosaic SVs"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
123 ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Structural variation with precise breakpoints"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
124 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Structural variation with imprecise breakpoints"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
125 ##INFO=<ID=MOSAIC,Number=0,Type=Flag,Description="Structural variation classified as putative mosaic"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
126 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of structural variation"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
127 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variation"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
128 ##INFO=<ID=CHR2,Number=1,Type=String,Description="Mate chromsome for BND SVs"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
129 ##INFO=<ID=SUPPORT,Number=1,Type=Integer,Description="Number of reads supporting the structural variation"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
130 ##INFO=<ID=SUPPORT_INLINE,Number=1,Type=Integer,Description="Number of reads supporting an INS/DEL SV (non-split events only)"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
131 ##INFO=<ID=SUPPORT_LONG,Number=1,Type=Integer,Description="Number of soft-clipped reads putatively supporting the long insertion SV"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
132 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of structural variation"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
133 ##INFO=<ID=STDEV_POS,Number=1,Type=Float,Description="Standard deviation of structural variation start position"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
134 ##INFO=<ID=STDEV_LEN,Number=1,Type=Float,Description="Standard deviation of structural variation length"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
135 ##INFO=<ID=COVERAGE,Number=.,Type=Float,Description="Coverages near upstream, start, center, end, downstream of structural variation"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
136 ##INFO=<ID=STRAND,Number=1,Type=String,Description="Strands of supporting reads for structural variant"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
137 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count, summed up over all samples"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
138 ##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description="List of read support for all samples"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
139 ##INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description="Number of reads that support the generated insertion (INS) consensus sequence"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
140 ##INFO=<ID=RNAMES,Number=.,Type=String,Description="Names of supporting reads (if enabled with --output-rnames)"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
141 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
142 ##INFO=<ID=NM,Number=.,Type=Float,Description="Mean number of query alignment length adjusted mismatches of supporting reads"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
143 ##INFO=<ID=PHASE,Number=.,Type=String,Description="Phasing information derived from supporting reads, represented as list of: HAPLOTYPE,PHASESET,HAPLOTYPE_SUPPORT,PHASESET_SUPPORT,HAPLOTYPE_FILTER,PHASESET_FILTER"> |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
144 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE |
09f5c6f3088a
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents:
0
diff
changeset
|
145 21 21492142 Sniffles2.DEL.0S14 N <DEL> 52 PASS PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492648;SUPPORT=48;COVERAGE=46,43,43,43,48;STRAND=+-;AF=1.000;STDEV_LEN=0.509;STDEV_POS=1.404 GT:GQ:DR:DV 1/1:60:0:48 |