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Dear Cancer IT group:
I downloaded the Nature Paper and supplementary data from the following website:
https://dcc.icgc.org/releases/PCAWG/consensus_sv
However, I find I am confused about the format and the interpretation. How to understand the structural variation with bedpe format?
For example, the first one is duplication, how to know which region is duplicated ? how many duplicates happened?
What does start1 and end1 mean? why they are always having 1b difference?
chrom1 start1 end1 chrom2 start2 end2 sv_id pe_support strand1 strand2 svclass 1 10428600 10428601 1 10582238 10582239 SVMERGE93 80 - + DUP 1 26939174 26939175 1 27518317 27518318 SVMERGE102 89 + - DEL 1 29834388 29834389 1 33723647 33723648 SVMERGE100 107 - - t2tINV 1 29834417 29834418 1 33723675 33723676 SVMERGE101 87 + + h2hINV 1 32728334 32728335 1 32845969 32845970 SVMERGE99 33 - + DUP 1 78236345 78236346 1 78427706 78427707 SVMERGE98 71 + - DEL 1 151858704 151858705 13 44927717 44927718 SVMERGE151 75 - + TRA 1 151873175 151873176 1 183511505 183511506 SVMERGE152 41 + - DEL 1 151887225 151887226 13 44703672 44703673 SVMERGE163 65 - - TRA
Thanks.
Shicheng
The text was updated successfully, but these errors were encountered:
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Dear Cancer IT group:
I downloaded the Nature Paper and supplementary data from the following website:
https://dcc.icgc.org/releases/PCAWG/consensus_sv
However, I find I am confused about the format and the interpretation. How to understand the structural variation with bedpe format?
For example, the first one is duplication, how to know which region is duplicated ? how many duplicates happened?
What does start1 and end1 mean? why they are always having 1b difference?
Thanks.
Shicheng
The text was updated successfully, but these errors were encountered: