Mercurial > repos > bgruening > nanopolish_methylation

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

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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
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--- a/test-data/t2-variants.vcf	Tue Jun 05 18:25:34 2018 -0400
+++ b/test-data/t2-variants.vcf	Wed Jun 19 03:45:24 2019 -0400
@@ -1,4 +1,5 @@
 ##fileformat=VCFv4.2
+##nanopolish_window=tig00000001:198000-202000
 ##INFO=<ID=TotalReads,Number=1,Type=Integer,Description="The number of event-space reads used to call the variant">
 ##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-space reads that support the variant">
 ##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant">
@@ -7,13 +8,4 @@
 ##INFO=<ID=SupportFractionByBase,Number=4,Type=Integer,Description="The fraction of reads supporting A,C,G,T at this position">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
-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
-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
-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
-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
-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
-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
-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
-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
-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
-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
+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