Mercurial > repos > bgruening > nanopolish_methylation

annotate test-data/variants.vcf @ 0:f9dadc362197 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
author bgruening
date Wed, 30 May 2018 11:55:55 -0400
parents
children 02e3c674d917
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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
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
2 ##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
3 ##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-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
4 ##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
5 ##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
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6 ##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele">
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
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diff changeset
7 ##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
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8 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
9 tig00000001 200061 . T TA 22.4 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.583757 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
10 tig00000001 200180 . C CA 30.6 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.596279 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
11 tig00000001 200484 . G GA 25.3 PASS TotalReads=63;AlleleCount=1;SupportFraction=0.569915 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
12 tig00000001 200672 . T TA 94.1 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.720712 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
13 tig00000001 200776 . C CA 82.3 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.71125 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
14 tig00000001 200796 . T TA 75.4 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.698132 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
15 tig00000001 201007 . A AG 31.0 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.604821 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
16 tig00000001 201216 . A AT 85.8 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.715932 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
17 tig00000001 201273 . G GT 25.2 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.588877 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
18 tig00000001 201554 . G GC 49.9 PASS TotalReads=76;AlleleCount=1;SupportFraction=0.632029 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
19 tig00000001 201588 . C CG 125.4 PASS TotalReads=75;AlleleCount=1;SupportFraction=0.660079 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
20 tig00000001 201712 . C CA 21.1 PASS TotalReads=74;AlleleCount=1;SupportFraction=0.57415 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
21 tig00000001 200061 . T TA 22.4 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.583757 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
22 tig00000001 200180 . C CA 30.6 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.596279 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
23 tig00000001 200484 . G GA 25.3 PASS TotalReads=63;AlleleCount=1;SupportFraction=0.569915 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
24 tig00000001 200672 . T TA 94.1 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.431464 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
25 tig00000001 200776 . C CA 82.3 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.362655 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
26 tig00000001 200796 . T TAA 117.1 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.544883 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
27 tig00000001 201007 . A AG 31.0 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.604821 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
28 tig00000001 201216 . A AT 85.8 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.457699 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
29 tig00000001 201273 . G GT 25.2 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.588877 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
30 tig00000001 201554 . G GC 49.9 PASS TotalReads=76;AlleleCount=1;SupportFraction=0.632029 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
31 tig00000001 201588 . C CG 125.4 PASS TotalReads=75;AlleleCount=1;SupportFraction=0.387616 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
32 tig00000001 201712 . C CA 21.1 PASS TotalReads=74;AlleleCount=1;SupportFraction=0.57415 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
33 tig00000001 200061 . T TA 22.4 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.583757 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
34 tig00000001 200180 . C CA 30.6 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.596279 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
35 tig00000001 200484 . G GA 25.3 PASS TotalReads=63;AlleleCount=1;SupportFraction=0.569915 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
36 tig00000001 200672 . T TA 94.1 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.431464 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
37 tig00000001 200776 . C CA 82.3 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.362655 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
38 tig00000001 200796 . T TAA 117.1 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.268565 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
39 tig00000001 201007 . A AG 31.0 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.604821 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
40 tig00000001 201216 . A AT 85.8 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.457699 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
41 tig00000001 201273 . G GT 25.2 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.588877 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
42 tig00000001 201554 . G GC 49.9 PASS TotalReads=76;AlleleCount=1;SupportFraction=0.632029 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
43 tig00000001 201588 . C CG 125.4 PASS TotalReads=75;AlleleCount=1;SupportFraction=0.387616 GT 1
f9dadc362197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff changeset
44 tig00000001 201712 . C CA 21.1 PASS TotalReads=74;AlleleCount=1;SupportFraction=0.57415 GT 1