Mercurial > repos > bgruening > nanopolish_methylation

annotate test-data/t2-variants.vcf @ 5:12efe2f03697 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"
author bgruening
date Fri, 29 May 2020 13:30:11 -0400
parents 02e3c674d917
children
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f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
1 ##fileformat=VCFv4.2
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02e3c674d917 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
bgruening
parents: 0
diff changeset
2 ##nanopolish_window=tig00000001:198000-202000
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f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
3 ##INFO=<ID=TotalReads,Number=1,Type=Integer,Description="The number of event-space reads used to call the variant">
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
4 ##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-space reads that support the variant">
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12efe2f03697 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"
bgruening
parents: 3
diff changeset
5 ##INFO=<ID=SupportFractionByStrand,Number=2,Type=Float,Description="Fraction of event-space reads that support the variant for each strand">
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f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
6 ##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant">
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
7 ##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description="The fraction of base-space reads that support the variant">
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
8 ##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele">
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12efe2f03697 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"
bgruening
parents: 3
diff changeset
9 ##INFO=<ID=StrandSupport,Number=4,Type=Integer,Description="Number of reads supporting the REF and ALT allele, by strand">
12efe2f03697 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"
bgruening
parents: 3
diff changeset
10 ##INFO=<ID=StrandFisherTest,Number=1,Type=Integer,Description="Strand bias fisher test">
12efe2f03697 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"
bgruening
parents: 3
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11 ##INFO=<ID=SOR,Number=1,Type=Float,Description="StrandOddsRatio test from GATK">
12efe2f03697 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"
bgruening
parents: 3
diff changeset
12 ##INFO=<ID=RefContext,Number=1,Type=String,Description="The reference sequence context surrounding the variant call">
12efe2f03697 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"
bgruening
parents: 3
diff changeset
13 ##INFO=<ID=SupportFractionByBase,Number=4,Type=Float,Description="The fraction of reads supporting A,C,G,T at this position">
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f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
14 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
15 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample