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#489 removed unused RF header
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REF+REFPAIR works except for the specific edge case of a concordant read pair that has an internal split read.
>>>>    >>>>------<<<<<
primary sup       primary (primaries are concordant)
         ^
         |
      breakpoint position
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Daniel Cameron committed May 14, 2021
1 parent 58ac7d8 commit e137d73
Showing 1 changed file with 1 addition and 1 deletion.
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
public enum VcfFormatAttributes {
REFERENCE_READ_COUNT ("REF", 1, VCFHeaderLineType.Integer, "Count of reads mapping across this breakend"),
REFERENCE_READPAIR_COUNT ("REFPAIR", 1, VCFHeaderLineType.Integer, "Count of reference read pairs spanning this breakend supporting the reference allele"),
REFERENCE_FRAGMENTS ("RF", 1, VCFHeaderLineType.Integer, "Reference fragments. Count of fragments supporting the reference allele and not the variant allele."),
//REFERENCE_FRAGMENTS ("RF", 1, VCFHeaderLineType.Integer, "Reference fragments. Count of fragments supporting the reference allele and not the variant allele."),
BREAKEND_QUAL ("BQ", 1, VCFHeaderLineType.Float, "Quality score of breakend evidence after evidence reallocation"),
BREAKPOINT_QUAL ("QUAL", 1, VCFHeaderLineType.Float, "Quality score of breakend evidence after evidence reallocation"),

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