Mercurial > repos > iuc > bbtools_bbmap
annotate test-data/cv_output.vcf @ 14:8015d7ab8357 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 46992fbb9d79da3d3c45b0c10f2936cf2af2dbcd
| author | iuc |
|---|---|
| date | Tue, 19 Nov 2024 14:47:35 +0000 |
| parents | 456d8ebb6a28 |
| children |
| rev | line source |
|---|---|
|
1
17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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1 ##fileformat=VCFv4.2 |
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13
456d8ebb6a28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
iuc
parents:
1
diff
changeset
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2 ##BBMapVersion=39.08 |
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1
17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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3 ##ploidy=2 |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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4 ##rarity=1.00000 |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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5 ##minallelefraction=0.10000 |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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6 ##reads=2207 |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
7 ##pairedReads=0 |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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8 ##properlyPairedReads=0 |
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13
456d8ebb6a28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
iuc
parents:
1
diff
changeset
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9 ##readLengthAvg=145.462 |
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1
17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
10 ##properPairRate=0.00000 |
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13
456d8ebb6a28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
iuc
parents:
1
diff
changeset
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11 ##totalQualityAvg=36.580 |
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1
17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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12 ##mapqAvg=43.348 |
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13
456d8ebb6a28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
iuc
parents:
1
diff
changeset
|
13 ##reference=/home/bag/projects/code/tools-iuc/tools/bbtools/test-data/NC_002945v4.fasta |
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1
17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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14 ##contig=<ID=NC_002945.4,length=7000> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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15 ##FILTER=<ID=FAIL,Description="Fail"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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16 ##FILTER=<ID=PASS,Description="Pass"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
17 ##INFO=<ID=SN,Number=1,Type=Integer,Description="Scaffold Number"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
18 ##INFO=<ID=STA,Number=1,Type=Integer,Description="Start"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
19 ##INFO=<ID=STO,Number=1,Type=Integer,Description="Stop"> |
|
17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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20 ##INFO=<ID=TYP,Number=1,Type=String,Description="Type"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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21 ##INFO=<ID=R1P,Number=1,Type=Integer,Description="Read1 Plus Count"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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22 ##INFO=<ID=R1M,Number=1,Type=Integer,Description="Read1 Minus Count"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
23 ##INFO=<ID=R2P,Number=1,Type=Integer,Description="Read2 Plus Count"> |
|
17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
24 ##INFO=<ID=R2M,Number=1,Type=Integer,Description="Read2 Minus Count"> |
|
17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
25 ##INFO=<ID=AD,Number=1,Type=Integer,Description="Allele Depth"> |
|
17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
26 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> |
|
17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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27 ##INFO=<ID=MCOV,Number=1,Type=Integer,Description="Minus Coverage"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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28 ##INFO=<ID=PPC,Number=1,Type=Integer,Description="Paired Count"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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29 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Fraction"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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30 ##INFO=<ID=RAF,Number=1,Type=Float,Description="Revised Allele Fraction"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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31 ##INFO=<ID=LS,Number=1,Type=Integer,Description="Length Sum"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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32 ##INFO=<ID=MQS,Number=1,Type=Integer,Description="MAPQ Sum"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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33 ##INFO=<ID=MQM,Number=1,Type=Integer,Description="MAPQ Max"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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34 ##INFO=<ID=BQS,Number=1,Type=Integer,Description="Base Quality Sum"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
35 ##INFO=<ID=BQM,Number=1,Type=Integer,Description="Base Quality Max"> |
|
17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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36 ##INFO=<ID=EDS,Number=1,Type=Integer,Description="End Distance Sum"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
37 ##INFO=<ID=EDM,Number=1,Type=Integer,Description="End Distance Max"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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38 ##INFO=<ID=IDS,Number=1,Type=Integer,Description="Identity Sum"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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39 ##INFO=<ID=IDM,Number=1,Type=Integer,Description="Identity Max"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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40 ##INFO=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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41 ##INFO=<ID=FLG,Number=1,Type=Integer,Description="Flagged"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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42 ##INFO=<ID=CED,Number=1,Type=Integer,Description="Contig End Distance"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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43 ##INFO=<ID=HMP,Number=1,Type=Integer,Description="Homopolymer Count"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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44 ##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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45 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Ref+, Ref-, Alt+, Alt-"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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46 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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47 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
48 ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Allele Depth"> |
|
17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
49 ##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele Fraction"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
50 ##FORMAT=<ID=RAF,Number=1,Type=Float,Description="Revised Allele Fraction"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
51 ##FORMAT=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count"> |
|
17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
52 ##FORMAT=<ID=FLG,Number=1,Type=Integer,Description="Flagged"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
|
53 ##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand Bias"> |
|
17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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54 ##FORMAT=<ID=SC,Number=1,Type=Float,Description="Score"> |
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17ad142b56e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff
changeset
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55 ##FORMAT=<ID=PF,Number=1,Type=String,Description="Pass Filter"> |
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13
456d8ebb6a28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
iuc
parents:
1
diff
changeset
|
56 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT dataset_4f1db038-76fe-46bc-a222-dfc4894a8ff2.dat |
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456d8ebb6a28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
iuc
parents:
1
diff
changeset
|
57 NC_002945.4 976327 . N T 22.21 PASS SN=0;STA=976326;STO=976327;TYP=SUB;R1P=2;R1M=0;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1;RAF=1;LS=292;MQS=77;MQM=40;BQS=48;BQM=24;EDS=111;EDM=65;IDS=1930;IDM=972;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1:1:0:0:0.9980:22.21:PASS |
|
456d8ebb6a28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
iuc
parents:
1
diff
changeset
|
58 NC_002945.4 1501932 . N C 27.20 PASS SN=0;STA=1501931;STO=1501932;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1;RAF=1;LS=292;MQS=88;MQM=44;BQS=64;BQM=39;EDS=74;EDM=38;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1:1:0:0:0.9980:27.20:PASS |
|
456d8ebb6a28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
iuc
parents:
1
diff
changeset
|
59 NC_002945.4 3380579 . N G 27.85 PASS SN=0;STA=3380578;STO=3380579;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1;RAF=1;LS=289;MQS=87;MQM=44;BQS=75;BQM=38;EDS=105;EDM=63;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1:1:0:0:0.9980:27.85:PASS |
|
456d8ebb6a28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
iuc
parents:
1
diff
changeset
|
60 NC_002945.4 3646293 . N A 23.34 PASS SN=0;STA=3646292;STO=3646293;TYP=SUB;R1P=1;R1M=1;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1;RAF=1;LS=291;MQS=86;MQM=44;BQS=76;BQM=38;EDS=44;EDM=31;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=1 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1:1:0:0:1:23.34:PASS |