Mercurial > repos > iuc > ivar_trim
annotate test-data/zika/Z52_a_pass.vcf @ 12:e3bb03cf207a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
author | iuc |
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date | Wed, 11 Jan 2023 09:55:20 +0000 |
parents | 364f4ffec275 |
children | 0893a1dbb807 |
rev | line source |
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7
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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1 ##fileformat=VCFv4.2 |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
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2 ##source=iVar |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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4 ##INFO=<ID=REF_DP,Number=1,Type=Integer,Description="Depth of reference base"> |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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5 ##INFO=<ID=REF_RV,Number=1,Type=Integer,Description="Depth of reference base on reverse reads"> |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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6 ##INFO=<ID=REF_QUAL,Number=1,Type=Integer,Description="Mean quality of reference base"> |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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7 ##INFO=<ID=ALT_DP,Number=1,Type=Integer,Description="Depth of alternate base"> |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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8 ##INFO=<ID=ALT_RV,Number=1,Type=Integer,Description="Deapth of alternate base on reverse reads"> |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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9 ##INFO=<ID=ALT_QUAL,Number=1,Type=Integer,Description="Mean quality of alternate base"> |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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10 ##INFO=<ID=AF,Number=1,Type=Float,Description="Frequency of alternate base"> |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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11 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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12 ##FILTER=<ID=PASS,Description="Result of p-value <= 0.05"> |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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13 ##FILTER=<ID=FAIL,Description="Result of p-value > 0.05"> |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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14 #CHROM POS ID REF ALT QUAL FILTER INFO |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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15 PRV 1682 . C T . PASS DP=1133;REF_DP=1097;REF_RV=984;REF_QUAL=37;ALT_DP=34;ALT_RV=33;ALT_QUAL=37;AF=0.0300088 |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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16 PRV 1965 . T G . PASS DP=365;REF_DP=302;REF_RV=113;REF_QUAL=37;ALT_DP=63;ALT_RV=25;ALT_QUAL=37;AF=0.172603 |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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17 PRV 2781 . T G . PASS DP=408;REF_DP=354;REF_RV=70;REF_QUAL=37;ALT_DP=48;ALT_RV=8;ALT_QUAL=36;AF=0.117647 |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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18 PRV 2922 . C T . PASS DP=275;REF_DP=264;REF_RV=0;REF_QUAL=36;ALT_DP=11;ALT_RV=0;ALT_QUAL=36;AF=0.04 |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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19 PRV 3148 . Y T . PASS DP=1707;REF_DP=0;REF_RV=0;REF_QUAL=0;ALT_DP=1324;ALT_RV=264;ALT_QUAL=36;AF=0.77563 |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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20 PRV 3148 . Y C . PASS DP=1707;REF_DP=0;REF_RV=0;REF_QUAL=0;ALT_DP=381;ALT_RV=75;ALT_QUAL=36;AF=0.223199 |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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21 PRV 3295 . A G . PASS DP=1040;REF_DP=1002;REF_RV=1002;REF_QUAL=35;ALT_DP=38;ALT_RV=38;ALT_QUAL=33;AF=0.0365385 |
12
e3bb03cf207a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
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22 PRV 5680 . C T . PASS DP=35;REF_DP=27;REF_RV=10;REF_QUAL=44;ALT_DP=8;ALT_RV=3;ALT_QUAL=46;AF=0.228571 |
7
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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23 PRV 7916 . C T . PASS DP=432;REF_DP=351;REF_RV=289;REF_QUAL=36;ALT_DP=81;ALT_RV=78;ALT_QUAL=37;AF=0.1875 |
364f4ffec275
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff
changeset
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24 PRV 9713 . C T . PASS DP=387;REF_DP=374;REF_RV=0;REF_QUAL=37;ALT_DP=13;ALT_RV=0;ALT_QUAL=35;AF=0.0335917 |