#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT MYSAMPLE
chr1 110 . N <DUP:TANDEM> 1 PASS END=125;SVLEN=16;iGenVar_SVLEN=4;SVTYPE=DUP GT ./.
chr1 181 . N <DUP:TANDEM> 1 PASS END=188;SVLEN=8;iGenVar_SVLEN=7;SVTYPE=DUP GT ./.
chr1 181 . N <DUP:TANDEM> 2 PASS END=188;SVLEN=8;iGenVar_SVLEN=8;SVTYPE=DUP GT ./.
chr1 509 . N <DUP:TANDEM> 1 PASS END=529;SVLEN=21;iGenVar_SVLEN=9;SVTYPE=DUP GT ./.
The real duplications are:
...GGG ATATATTT ATATATTT TAC... <- Tandem Duplication ref: (180, 188] tandem duplicated
...GCG TAACCCGGG TAACCCGGG TAACCCGGG TAACCCGGG TAACCCGGG TAC... Duplication in reference and read covered by SA tag ref: (509, 527] with copynumber=5
Our results from the mini example are giving us:
The real duplications are: ...GGG ATATATTT ATATATTT TAC... <- Tandem Duplication ref: (180, 188] tandem duplicated ...GCG TAACCCGGG TAACCCGGG TAACCCGGG TAACCCGGG TAACCCGGG TAC... Duplication in reference and read covered by SA tag ref: (509, 527] with copynumber=5
Jörg also raised the question why we calculate the sv length as difference +2. _Originally posted by @joergi-w in https://github.com/seqan/iGenVar/pull/223#discussion_r925268668_