Mercurial > repos > bgruening > nanopolish_methylation

comparison test-data/t2-variants.vcf @ 3:02e3c674d917 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
author bgruening
date Wed, 19 Jun 2019 03:45:24 -0400
parents f9dadc362197
children 12efe2f03697
comparison
equal deleted inserted replaced
2:07cf146e8964 3:02e3c674d917
1 ##fileformat=VCFv4.2 1 ##fileformat=VCFv4.2
2 ##nanopolish_window=tig00000001:198000-202000
2 ##INFO=<ID=TotalReads,Number=1,Type=Integer,Description="The number of event-space reads used to call the variant"> 3 ##INFO=<ID=TotalReads,Number=1,Type=Integer,Description="The number of event-space reads used to call the variant">
3 ##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-space reads that support the variant"> 4 ##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-space reads that support the variant">
4 ##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant"> 5 ##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant">
5 ##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description="The fraction of base-space reads that support the variant"> 6 ##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description="The fraction of base-space reads that support the variant">
6 ##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele"> 7 ##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele">
7 ##INFO=<ID=SupportFractionByBase,Number=4,Type=Integer,Description="The fraction of reads supporting A,C,G,T at this position"> 8 ##INFO=<ID=SupportFractionByBase,Number=4,Type=Integer,Description="The fraction of reads supporting A,C,G,T at this position">
8 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 9 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
9 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample 10 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
10 tig00000001 200180 . C CA 30.6 PASS BaseCalledReadsWithVariant=18;BaseCalledFraction=0.268657;TotalReads=66;AlleleCount=2;SupportFraction=0.596279;SupportFractionByBase=0.042,0.831,0.008,0.119 GT 1/1 11 tig00000001 198435 . G A 22.3 PASS BaseCalledReadsWithVariant=10;BaseCalledFraction=0.238095;TotalReads=42;AlleleCount=1;SupportFraction=0.388965;SupportFractionByBase=0.210,0.030,0.718,0.041 GT 0/1
11 tig00000001 200208 . GA G 28.2 PASS BaseCalledReadsWithVariant=15;BaseCalledFraction=0.223881;TotalReads=66;AlleleCount=1;SupportFraction=0.392611;SupportFractionByBase=0.180,0.007,0.780,0.034 GT 0/1
12 tig00000001 200484 . G GA 37.7 PASS BaseCalledReadsWithVariant=17;BaseCalledFraction=0.261538;TotalReads=63;AlleleCount=1;SupportFraction=0.569915;SupportFractionByBase=0.049,0.009,0.928,0.014 GT 0/1
13 tig00000001 200776 . C CA 82.3 PASS BaseCalledReadsWithVariant=24;BaseCalledFraction=0.358209;TotalReads=67;AlleleCount=2;SupportFraction=0.71125;SupportFractionByBase=0.039,0.883,0.046,0.032 GT 1/1
14 tig00000001 200796 . T TA 82.1 PASS BaseCalledReadsWithVariant=17;BaseCalledFraction=0.253731;TotalReads=66;AlleleCount=2;SupportFraction=0.697381;SupportFractionByBase=0.037,0.148,0.018,0.797 GT 1/1
15 tig00000001 200804 . TA T 82.1 PASS BaseCalledReadsWithVariant=20;BaseCalledFraction=0.298507;TotalReads=66;AlleleCount=1;SupportFraction=0.405017;SupportFractionByBase=0.100,0.185,0.006,0.709 GT 0/1
16 tig00000001 200966 . CA C 45.5 PASS BaseCalledReadsWithVariant=16;BaseCalledFraction=0.242424;TotalReads=64;AlleleCount=1;SupportFraction=0.383448;SupportFractionByBase=0.039,0.740,0.061,0.159 GT 0/1
17 tig00000001 201216 . A AT 85.8 PASS BaseCalledReadsWithVariant=24;BaseCalledFraction=0.352941;TotalReads=67;AlleleCount=2;SupportFraction=0.715932;SupportFractionByBase=0.908,0.004,0.026,0.061 GT 1/1
18 tig00000001 201554 . G GC 50.2 PASS BaseCalledReadsWithVariant=20;BaseCalledFraction=0.263158;TotalReads=76;AlleleCount=2;SupportFraction=0.632478;SupportFractionByBase=0.090,0.047,0.821,0.042 GT 1/1
19 tig00000001 201712 . C CA 29.7 PASS BaseCalledReadsWithVariant=21;BaseCalledFraction=0.272727;TotalReads=74;AlleleCount=1;SupportFraction=0.57415;SupportFractionByBase=0.046,0.747,0.074,0.133 GT 0/1