Mercurial > repos > dfornika > ivar_variants_to_vcf

annotate test-data/SAMEA6808195-variants.vcf @ 0:c87f6ad32fd8 draft default tip

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"planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
author dfornika
date Fri, 05 Jun 2020 05:10:05 +0000
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c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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1 ##fileformat=VCFv4.2
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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2 ##source=iVar
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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4 ##FILTER=<ID=PASS,Description="Result of p-value <= 0.05">
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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5 ##FILTER=<ID=FAIL,Description="Result of p-value > 0.05">
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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7 ##FORMAT=<ID=REF_DP,Number=1,Type=Integer,Description="Depth of reference base">
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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8 ##FORMAT=<ID=REF_RV,Number=1,Type=Integer,Description="Depth of reference base on reverse reads">
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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9 ##FORMAT=<ID=REF_QUAL,Number=1,Type=Integer,Description="Mean quality of reference base">
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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10 ##FORMAT=<ID=ALT_DP,Number=1,Type=Integer,Description="Depth of alternate base">
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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11 ##FORMAT=<ID=ALT_RV,Number=1,Type=Integer,Description="Deapth of alternate base on reverse reads">
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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12 ##FORMAT=<ID=ALT_QUAL,Number=1,Type=String,Description="Mean quality of alternate base">
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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13 ##FORMAT=<ID=ALT_FREQ,Number=1,Type=String,Description="Frequency of alternate base">
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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14 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMEA6808195-variants
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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15 MN908947.3 30 . A T . PASS DP=53 GT:REF_DP:REF_RV:REF_QUAL:ALT_DP:ALT_RV:ALT_QUAL:ALT_FREQ 1:23:10:38:30:0:33:0.566038
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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16 MN908947.3 228 . C T . PASS DP=3932 GT:REF_DP:REF_RV:REF_QUAL:ALT_DP:ALT_RV:ALT_QUAL:ALT_FREQ 1:3:0:47:3929:107:73:0.999237
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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17 MN908947.3 241 . C T . PASS DP=3943 GT:REF_DP:REF_RV:REF_QUAL:ALT_DP:ALT_RV:ALT_QUAL:ALT_FREQ 1:0:0:0:3943:127:72:1
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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18 MN908947.3 3037 . C T . PASS DP=1713 GT:REF_DP:REF_RV:REF_QUAL:ALT_DP:ALT_RV:ALT_QUAL:ALT_FREQ 1:0:0:0:1713:100:74:1
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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19 MN908947.3 14408 . C T . PASS DP=6480 GT:REF_DP:REF_RV:REF_QUAL:ALT_DP:ALT_RV:ALT_QUAL:ALT_FREQ 1:2:0:53:6478:209:75:0.999691
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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20 MN908947.3 17126 . T C . PASS DP=11854 GT:REF_DP:REF_RV:REF_QUAL:ALT_DP:ALT_RV:ALT_QUAL:ALT_FREQ 1:3:0:39:11851:4693:38:0.999747
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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21 MN908947.3 20268 . A G . PASS DP=327 GT:REF_DP:REF_RV:REF_QUAL:ALT_DP:ALT_RV:ALT_QUAL:ALT_FREQ 1:0:0:0:327:1:38:1
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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22 MN908947.3 23403 . A G . PASS DP=5968 GT:REF_DP:REF_RV:REF_QUAL:ALT_DP:ALT_RV:ALT_QUAL:ALT_FREQ 1:1:1:39:5964:5939:38:0.99933
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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23 MN908947.3 28770 . C T . PASS DP=1661 GT:REF_DP:REF_RV:REF_QUAL:ALT_DP:ALT_RV:ALT_QUAL:ALT_FREQ 1:148:141:36:1513:40:38:0.910897