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Notes on SV representation
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SV_Representations.md

Background

BEDPE coordinates refer to a genomic position, but it is unclear to me what position (relative to an SV) they are intended to convey. This is illustrated in the case where we know precisely where the breakpoints are.

Potential Reporting Conventions

  1. Affected Bases (AFF)
  2. Left of the breakpoint (LOB)
  3. Right of the breakpoint (ROB)
  4. Exact breakpoint (BPT)
  5. Last-aligned Base (LAB)

Events to support

  1. Simple Deletions
  2. Simple Insertions
  3. Range Math on coordinates
  4. Balanced Translocations/Inversion
  5. Telomeric Deletions
  6. Unbalanced Translocations/Inversions
  7. Telomeric Insertions

Simple Deletions

Alignment for fictional 5bp DEL

We will call the chromosome below 'chr'.

Plain alignment:

REF ACGTGCC
ALT A-----C

With 0-based coordinates (BED):

    0123456
REF ACGTGCC
ALT A-----C

With 1-based coordinates (VCF):

    1234567
REF ACGTGCC
ALT A-----C

VCF Entry as a precise SV

Assume chromosome name is 1

chr 1 . ACGTGC  A . PASS  SVTYPE=DEL;END=6

VCF Entry as BND entries (again, precise)

chr 1 . A A[chr:7[  . PASS  SVTYPE=BND
chr 7 . C ]chr:1]C  . PASS  SVTYPE=BND

BEDPE Entry options

AFF

The coordinates label the first and last deleted bases.

chr 1 2 chr 5 6
  • Note that for range arithmetic, the length would be end2 - start1

LOB

The coordinates label the base to the left of the breakpoint(s).

chr 0 1 chr 5 6
  • Note that for range arithmetic, the length would be start2 - start1 or end2 - end1 but that start2 - end1 and end2 - start1 would not give the length.

ROB

The coordinates label the base to the right of the breakpoint(s).

chr 1 2 chr 6 7
  • Note that for range arithmetic, the length would be start2 - start1 or end2 - end1 but that start2 - end1 and end2 - start1 would not give the length.

BPT

Coordinates are 0-length ranges specifying the position of the breakpoint.

chr 1 1 chr 6 6
  • Note that for range arithmetic, the length is the same no matter which coordinates you use between the two coordinate sets.

LAB

Coordinates specify the "last-aligned base" as in VCF

chr 0 1 chr 6 7
  • Note that for range arithmetic, the length would be start2 - end1 or end2 - end1 - 1 or start2 - start1 -1.

Simple Insertions

Alignment for fictional 5bp INS

We will call the chromosome below 'chr'.

Plain alignment:

REF A-----C
ALT ACGTGCC

With 0-based coordinates (BED):

    0123456
REF A-----C
ALT ACGTGCC

With 1-based coordinates (VCF):

    1234567
REF A-----C
ALT ACGTGCC

VCF Entry as a precise SV

Assume chromosome name is chr

chr 1 . A  ACGTGC . PASS  SVTYPE=INS;END=1

VCF Entry as BND entries (again, precise)

chr 1 . A ACGTGC[chr:2[  . PASS  SVTYPE=BND
chr 2 . C ]chr:1]CGTGCC  . PASS  SVTYPE=BND

BEDPE Entry options

Note that range arithmetic would not apply to these cases as insertion size has no effect on the coordinates of the reference.

AFF

This seems to make no sense. What base is the affected-based? You would have to fall back to either leftmost or rightmost base in this case. See those below.

LOB

chr 0   1 chr 0   1

ROB

chr 1   2   chr 1   2

BPT

chr 1   1   chr 1   1

LAB

chr 0   1   chr 1   2

Reciprocal Translocations/Inversions

Will only consider inversions as those actually have some range math applications that may prove illustrative.

Alignment for fictional 5bp INV

We will call the chromosome below 'chr'

Plain alignment:

REF ATGTGCC
ALT AGCACAC

With 0-based coordinates (BED):

    0123456
REF ATGTGCC
ALT AGCACAC

With 1-based coordinates (VCF):

    1234567
REF ATGTGCC
ALT AGCACAC

VCF Entry as a precise SV

chr 1   .   ATGTGC   AGCACA   .   PASS    SVTYPE=INV;END=6

VCF Entries as a BND. Includes ALL breakends

chr 1   .   A   A]chr:6]    .   PASS    SVTYPE=BND
chr 2   .   T   [chr:7[T    .   PASS    SVTYPE=BND
chr 6   .   C   C]chr:1]    .   PASS    SVTYPE=BND
chr 7   .   C   [chr:2[C    .   PASS    SVTYPE=BND

BEDPE Entry options

AFF

chr 1   2   chr 5   6
  • Note for range arithmetic, the length would be end2 - start1

LOB

chr 0   1   chr 5   6
  • Note that for range operations, the length is end2 - end1.

ROB

chr 1   2   chr 6   7
  • Note that for range operations, the length is end2 - end1.

BPT

chr 1   1   chr 6   6
  • Note that for the range arithmetic, the length is the same no matter which coordinates you use.

LAB

chr 0   1   chr 6   7
  • Note that for the range arithmetic, the length end2 - start2 - 1.

Telomeric Deletion (Right)

Alignment for fictional telomeric DEL

We will call the chromosome below 'chr'.

Plain alignment:

REF ACGTGCC
ALT A------

With 0-based coordinates (BED):

    0123456
REF ACGTGCC
ALT A------

With 1-based coordinates (VCF):

    1234567
REF ACGTGCC
ALT A------

VCF Entry as a precise SV

Assume chromosome name is 1

chr 1 . A  <DEL> . PASS  SVTYPE=DEL;END=7

VCF Entry as BND entries (again, precise)

chr 1 . A .[chr:8[  . PASS  SVTYPE=BND
chr 8 . N ]chr:1].  . PASS  SVTYPE=BND

BEDPE Entry options

AFF

The coordinates label the first and last deleted bases.

chr 1 2 chr 6 7
  • Note that for range arithmetic, the length would be end2 - start1

LOB

The coordinates label the base to the left of the breakpoint(s).

chr 0 1 chr 6 7
  • Note that for range arithmetic, the length would be end2 - end1

ROB

The coordinates label the base to the right of the breakpoint(s). It would have to be allowed or hacked to go greater than the length of the reference for BED

chr 1 2 chr 7 8
  • Note that for range arithmetic, the length would be start2 - start1 or end2 - end1 but that start2 - end1 and end2 - start1 would not give the length.

BPT

Coordinates are 0-length ranges specifying the position of the breakpoint.

chr 1   1 chr 7   7
  • Note that for range arithmetic, the length is the same no matter which coordinates you use between the two coordinate sets.

LAB

Coordinates specify the "last-aligned base" as in VCF. This would also have to allow for virtual bases off the end of the reference

chr 0 1 chr 7 8
  • Note that for range arithmetic, the length would be start2 - start1 - 1 or end2 - end1 -1.

Telomeric Deletion (Left)

Alignment for fictional telomeric DEL

We will call the chromosome below 'chr'.

Plain alignment:

REF ACGTGCC
ALT ------C

With 0-based coordinates (BED):

    0123456
REF ACGTGCC
ALT ------C

With 1-based coordinates (VCF):

    1234567
REF ACGTGCC
ALT ------C

VCF Entry as a precise SV

Assume chromosome name is 1

chr 0 . N  <DEL> . PASS  SVTYPE=DEL;END=6

VCF Entry as BND entries (again, precise)

chr 0 . N .[chr:7[  . PASS  SVTYPE=BND
chr 7 . C ]chr:0]C  . PASS  SVTYPE=BND

BEDPE Entry options

AFF

The coordinates label the first and last deleted bases.

chr 0 1 chr 5 6
  • Note that for range arithmetic, the length would be end2 - start1

LOB

The coordinates label the base to the left of the breakpoint(s). This breaks for this variant type.

ROB

The coordinates label the base to the right of the breakpoint(s).

chr 0 1 chr 6 7
  • Note that for range arithmetic, the length would be start2 - start1 or end2 - end1 but that start2 - end1 and end2 - start1 would not give the length.

BPT

Coordinates are 0-length ranges specifying the position of the breakpoint.

chr 0 0 chr 6 6
  • Note that for range arithmetic, the length is the same no matter which coordinates you use between the two coordinate sets.

LAB

Coordinates specify the "last-aligned base" as in VCF. This breaks for the same reason as left-most base.

Unbalanced Translocation

In VCF, these have to be explicitly labeled as a pair.

VCF Entry as BND entries (from VCF spec)

chr2 321681 bnd_W G G[chr13:123460[     .   PASS  SVTYPE=BND;PARID=bnd_V;MATEID=bnd_X
chr2 321682 bnd_V T ]chr13:123456]T     .   PASS  SVTYPE=BND;PARID=bnd_W;MATEID=bnd_U
chr13 123456 bnd_U C C[chr2:321682[     .   PASS  SVTYPE=BND;PARID=bnd_X;MATEID=bnd_V
chr13 123460 bnd_X A ]chr2:321681]A     .   PASS  SVTYPE=BND;PARID=bnd_U;MATEID=bnd_W

BEDPE Entry options

AFF

The coordinates label the first and last bases affected. Not clear what this means here. I contend it is invalid and you'd have to fallback to one of the other methodologies below.

LOB

The coordinates label the base to the left of the breakpoint(s).

chr2 321680 321681  chr13   123458  123459
chr2    321680  321681  chr13   123455  123456
chr13 123455    123456  chr2    321680  321681
chr13 123458    123459  chr2    321680  321681

ROB

The coordinates label the base to the right of the breakpoint(s).

chr2 321681 321682  chr13   123459  123460
chr2    321682  321683  chr13   123456  123457
chr13 123456    123457  chr2    321681  321682
chr13 123459    123460  chr2    321681  321682

BPT

Coordinates are 0-length ranges specifying the position of the breakpoint.

chr2 321681 321681  chr13   123459  123459
chr2    321681  321681  chr13   123456  123456

LAB

Coordinates specify the "last-aligned base" as in VCF.

chr2 321680 321681  chr13   123459  123460
chr2    321681  321682  chr13   123455  123456
chr13 123455    123456  chr2    321681  321682
chr13 123459    123460  chr2    321680  321681

Telomeric Insertions (Left)

Alignment for fictional telomeric INS (on left)

We will call the chromosome below 'chr'.

Plain alignment:

REF --ACGTGCC
ALT GCACGTGCC

With 0-based coordinates (BED):

      0123456
REF --ACGTGCC
ALT GCACGTGCC

With 1-based coordinates (VCF):

      1234567
REF --ACGTGCC
ALT GCACGTGCC

VCF Entry as a precise SV

Assume chromosome name is 1

chr 0 . N  <INS> . PASS  SVTYPE=INS;END=0

VCF Entry as BND entries (again, precise)

chr 0 . N .[ctg1:1[  . PASS  SVTYPE=BND
chr 1 . A ]ctg1:1000]A  . PASS  SVTYPE=BND

BEDPE Entry options

AFF

The coordinates label the first and last affected bases. Would have to label the base before the insertion. Can't do this in BED.

LOB

The coordinates label the base to the left of the breakpoint(s). This breaks for this variant type.

ROB

The coordinates label the base to the right of the breakpoint(s).

chr 0 1 chr 0 1

BPT

Coordinates are 0-length ranges specifying the position of the breakpoint.

chr 0 0 chr 0 0

LAB

Coordinates specify the "last-aligned base" as in VCF. This breaks for the same reason as left-most base.

Telomeric Insertions (Right)

Alignment for fictional telomeric INS (on left)

We will call the chromosome below 'chr'.

Plain alignment:

REF ACGTGCC--
ALT ACGTGCCGC

With 0-based coordinates (BED):

    0123456  
REF ACGTGCC--
ALT ACGTGCCGC

With 1-based coordinates (VCF):

    1234567  
REF ACGTGCC--
ALT ACGTGCCGC

VCF Entry as a precise SV

Assume chromosome name is 1

chr 7 . C  CGC . PASS  SVTYPE=INS;END=7

VCF Entry as BND entries (again, precise)

chr 7 . C C[ctg1:1[  . PASS  SVTYPE=BND
chr 8 . N ]ctg1:1000].  . PASS  SVTYPE=BND

BEDPE Entry options

AFF

The coordinates label the first and last affected bases. For insertions this could/should be the base to the left of the event.

chr 6 7 chr 6 7

LOB

The coordinates label the base to the left of the breakpoint(s).

chr 6 7 chr 6 7

ROB

The coordinates label the base to the right of the breakpoint(s).

chr 7 8 chr 7 8

BPT

Coordinates are 0-length ranges specifying the position of the breakpoint.

chr 7 7 chr 7 7

LAB

Coordinates specify the "last-aligned base" as in VCF.

chr 6 7 chr 6 7
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