APP Results

Notes

• This only compares SVs that made the VCF file and that were converted to BED. CNVs, translocations, aneuploidy, and complex SVs are not present in the VCF. This compares mainly insertion, deletions, and duplications.
  
• Intersect means a filter was applied. If file A intersects file B then file B is used as a filter. So, unique features in A remain and any overlapping regions in B are removed.
  
• Overlap means the overlapping features were counted. So, if file A, with 20 entries, overlaps file B, with 100 entries, then the output is the 20 entries from file A with an additional column that tells you how many overlaps are with file B.
  

APP_pos_1_parsed_info

This is APP_pos_1 before any filtering applied.

## [1] "Number of SVs:  597"

APP_pos_2_parsed_info

## [1] "Number of SVs:  591"

APP_neg_1_parsed_info

This is APP_pos_2 before any filtering applied.

## [1] "Number of SVs:  627"

APP_neg_2_parsed_info

This is APP_neg_1 before any filtering applied.

## [1] "Number of SVs:  612"

APP_pos_1_intersect_neg_merged

## [1] "Number of SVs:  89"

## 
##  chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19  chr2 chr20 
##     1     4     1     3     4     2     4     2     1     2     3     5     5 
## chr21  chr3  chr4  chr5  chr6  chr7  chr9 
##    29     2     1     3     3    10     4

APP_pos_2_intersect_neg_merged

## [1] "Number of SVs:  92"

## 
##  chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19  chr2 chr20 
##     8     5     2     1     2     2     5     1     1     1     4     1     5 
## chr21  chr3  chr4  chr5  chr6  chr7  chr8  chr9 
##    31     3     3     4     2     5     4     2

APP_pos_1_intersect_neg_1

## [1] "Number of SVs:  107"

## 
##  chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19  chr2 chr20 
##     1     4     1     3     4     3     6     3     1     2     3     5    11 
## chr21  chr3  chr4  chr5  chr6  chr7  chr8  chr9 
##    32     2     2     4     4    11     1     4

APP_pos_1_intersect_neg_2

## [1] "Number of SVs:  141"

## 
##  chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19  chr2 chr20 
##     9     6     3     2     2     3     7     1     1     1     4     1     7 
## chr21  chr3  chr4  chr5  chr6  chr7  chr8  chr9 
##    63     5     4     5     3     8     4     2

APP_neg_1_intersect_neg_2

## [1] "Number of SVs:  151"

## 
##  chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr19  chr2 chr20 chr21 
##     9     5     3     6     4     5     6     1     3     2     4     7    64 
##  chr3  chr4  chr5  chr6  chr7  chr8 
##     5     6     4     5    10     2

APP_neg_2_intersect_neg_1

## [1] "Number of SVs:  103"

## 
##  chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18  chr2 chr20 chr21 
##     1     2     3     2     1     4     7     5     4     1     3     9    21 
##  chr3  chr4  chr5  chr6  chr7  chr8  chr9 
##     9     6     2     5    11     6     1