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output xls and vcf file #10

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tgong1 opened this issue Jul 26, 2018 · 0 comments
Open

output xls and vcf file #10

tgong1 opened this issue Jul 26, 2018 · 0 comments

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@tgong1
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tgong1 commented Jul 26, 2018

I have two questions about the output files:

  1. I found the POS and END in vcf file are not same as it reported in xls files.
    e.g. in VCF
    CHROM POS END SVLEN SVTYPE
    chr1 10933 181382 170450 DEL
    in DEL.xls
    SVStart SVEnd Refstart1 Refend1 Refstart2 Refend2
    14974 180994 10465 14973 180995 185494
    Which output file I should use if I need the SV position information?

  2. SVs with SVTYPE as BND have ISVTYPE as INVB or TTLC.
    I'm wondering the difference between those two? Can I see INVB as intra-chromosomal translocation and TTLC as inter-chromosomal translocation?

Thank you!

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