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jazdrv / dnaTools

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calls with . for derived need to discern what they're negative for (ie: L48) #25

Closed jazdrv closed 6 years ago

jazdrv commented 6 years ago

ie: 21450311 G . PASS 33.1996 59.8263 76 1 0/0 (which is in Iain's VCF)

this should be L48-

whereas the variant def for L48+ is 21450311 G T

vID=403655 [L48 G/T] should be the same as vID=742789 [G/]. All that 742789 is is L48-.

So it looks like there's something to do with how we treat negative variants that needs changed. 0/0 is the ancestral allele (except for reference positives). So anyone with 21450311 with alt=T and genotype=1/1 should be L48+; anyone with 21450311 and genotype=0/0 should be L48-.

Zaks-MacBook-Pro:redux2 jazdrv$ r2 -vai 742789
Beginning run [14:29:08]
beg MatrixData restore: 0.681121
end MatrixData restore: 0.895585

+---------------------------------------------------------------------------------------------------------+
| vix  build  name    id      pos     anc  der  dupeP  nouse  pID   kix   kit    assign  geno  bed  mxval |
+---------------------------------------------------------------------------------------------------------+
|  -   hg38   -     742789  21450311   G    .     N      N     11    0   293507   None   None   0     -   |
|  -   hg38   -     742789  21450311   G    .     N      N    1320   1   224096    1     0/0    0     -   |
|  -   hg38   -     742789  21450311   G    .     N      N     4     2   510668   None   None   0     -   |
|  -   hg38   -     742789  21450311   G    .     N      N     12    3   122898   None   None   1     -   |
|  -   hg38   -     742789  21450311   G    .     N      N    1040   4   120386    1     0/0    0     -   |
|  -   hg38   -     742789  21450311   G    .     N      N    1237   5   124134   None   None   0     -   |
|  -   hg38   -     742789  21450311   G    .     N      N    1799   6   22654     1     0/0    0     -   |
|  -   hg38   -     742789  21450311   G    .     N      N     1     7   B30884   None   None   0     -   |
|  -   hg38   -     742789  21450311   G    .     N      N     2     8   637069   None   None   0     -   |
|  -   hg38   -     742789  21450311   G    .     N      N     5     9   499807   None   None   0     -   |
|  -   hg38   -     742789  21450311   G    .     N      N     13   10   521793   None   None   0     -   |
|  -   hg38   -     742789  21450311   G    .     N      N    867   11   163973   None   None   0     -   |
|  -   hg38   -     742789  21450311   G    .     N      N    1048  12   N4826     1     0/0    0     -   |
|  -   hg38   -     742789  21450311   G    .     N      N    1705  13   216600    1     0/0    0     -   |
|  -   hg38   -     742789  21450311   G    .     N      N    1745  14    5962     1     0/0    0     -   |
|  -   hg38   -     742789  21450311   G    .     N      N     3    15   177312    1     0/0    0     -   |
+---------------------------------------------------------------------------------------------------------+
Zaks-MacBook-Pro:redux2 jazdrv$ r2 -van L48
Beginning run [14:35:44]
beg MatrixData restore: 0.70176
end MatrixData restore: 0.905231

+---------------------------------------------------------------------------------------------------------+
| vix  build  name    id      pos     anc  der  dupeP  nouse  pID   kix   kit    assign  geno  bed  mxval |
+---------------------------------------------------------------------------------------------------------+
|  -   hg38   L48   403655  21450311   G    T     N      P     11    0   293507    1     1/1    0     -   |
|  -   hg38   L48   403655  21450311   G    T     N      P    1320   1   224096   None   None   0     -   |
|  -   hg38   L48   403655  21450311   G    T     N      P     4     2   510668    1     1/1    0     -   |
|  -   hg38   L48   403655  21450311   G    T     N      P     12    3   122898    1     1/1    1     -   |
|  -   hg38   L48   403655  21450311   G    T     N      P    1040   4   120386   None   None   0     -   |
|  -   hg38   L48   403655  21450311   G    T     N      P    1237   5   124134    1     1/1    0     -   |
|  -   hg38   L48   403655  21450311   G    T     N      P    1799   6   22654    None   None   0     -   |
|  -   hg38   L48   403655  21450311   G    T     N      P     1     7   B30884    1     1/1    0     -   |
|  -   hg38   L48   403655  21450311   G    T     N      P     2     8   637069    1     1/1    0     -   |
|  -   hg38   L48   403655  21450311   G    T     N      P     5     9   499807    1     1/1    0     -   |
|  -   hg38   L48   403655  21450311   G    T     N      P     13   10   521793    1     1/1    0     -   |
|  -   hg38   L48   403655  21450311   G    T     N      P    867   11   163973    1     1/1    0     -   |
|  -   hg38   L48   403655  21450311   G    T     N      P    1048  12   N4826    None   None   0     -   |
|  -   hg38   L48   403655  21450311   G    T     N      P    1705  13   216600   None   None   0     -   |
|  -   hg38   L48   403655  21450311   G    T     N      P    1745  14    5962    None   None   0     -   |
|  -   hg38   L48   403655  21450311   G    T     N      P     3    15   177312   None   None   0     -   |
+---------------------------------------------------------------------------------------------------------+
jazdrv commented 6 years ago

Just pushed this in:

9049af2 - Zak Jones, 53 minutes ago : issue #25 - some sql modifications to deal with the calls with . for derived issue

jeftreece commented 6 years ago

Does not apply to master branch after merge #38