diff test-data/t2-variants.vcf @ 5:d21b141aecc8 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit f325ca2ced02af231abfb08700aae1da6824c9ab"

--- a/test-data/t2-variants.vcf	Sun Jun 23 05:03:27 2019 -0400
+++ b/test-data/t2-variants.vcf	Thu Apr 30 22:51:16 2020 +0000
@@ -2,10 +2,14 @@
 ##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=SupportFractionByStrand,Number=2,Type=Float,Description="Fraction of event-space reads that support the variant for each strand">
 ##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant">
 ##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description="The fraction of base-space reads that support the variant">
 ##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele">
-##INFO=<ID=SupportFractionByBase,Number=4,Type=Integer,Description="The fraction of reads supporting A,C,G,T at this position">
+##INFO=<ID=StrandSupport,Number=4,Type=Integer,Description="Number of reads supporting the REF and ALT allele, by strand">
+##INFO=<ID=StrandFisherTest,Number=1,Type=Integer,Description="Strand bias fisher test">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="StrandOddsRatio test from GATK">
+##INFO=<ID=RefContext,Number=1,Type=String,Description="The reference sequence context surrounding the variant call">
+##INFO=<ID=SupportFractionByBase,Number=4,Type=Float,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	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