changes to run variant calling

aryeelab · May 2, 2018 · 8eabc66 · 8eabc66
1 parent 1a27105
commit 8eabc66
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diff --git a/test/data/variants/EMX1_Variants.txt b/test/data/variants/EMX1_Variants.txt
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+Chromosome	Start	End	Name	ReadCount	Variant_WindowSequence	Variant.Site.SubstitutionsOnly.Sequence	Variant.Site.SubstitutionsOnly.NumSubstitutions	Variant.Site.SubstitutionsOnly.Strand	Variant.Site.GapsAllowed.Sequence	Variant.Site.GapsAllowed.Length	Variant.Site.GapsAllowed.Substitutions	Variant.Site.GapsAllowed.Insertions	Variant.Site.GapsAllowed.Deletions	Variant.Site.GapsAllowed.Strand	Cell	Targetsite	TargetSequence	Variant.RealignedTargetSequence	Reference	Variant	Genotype	Quality
diff --git a/test/data/variants/EMX1_mpileupCall.txt b/test/data/variants/EMX1_mpileupCall.txt
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+targetsite	site_name	chromosome	one_based_position	reference	variant	quality	genotype	depth	PL
+EMX1	EMX1_chr1:236259170-236261754_1486_7	1:236259170-236261754	1472	C	T	134.008	0|1	368	164_0_255
+EMX1	EMX1_chr1:236259170-236261754_1486_7	1:236259170-236261754	1474	A	G	60.0073	0|1	316	90_0_255
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		Chromosome Start End Name ReadCount Variant_WindowSequence Variant.Site.SubstitutionsOnly.Sequence Variant.Site.SubstitutionsOnly.NumSubstitutions Variant.Site.SubstitutionsOnly.Strand Variant.Site.GapsAllowed.Sequence Variant.Site.GapsAllowed.Length Variant.Site.GapsAllowed.Substitutions Variant.Site.GapsAllowed.Insertions Variant.Site.GapsAllowed.Deletions Variant.Site.GapsAllowed.Strand Cell Targetsite TargetSequence Variant.RealignedTargetSequence Reference Variant Genotype Quality