events

[tanasa]

Hi everyone.

I am running Jabba and gGnome on two breast cancer lines MCF-7 and HCC1954, starting with the bam files of CCLE consortium. The issue is that gg$edges are blank, and the events() function calls 0 type of events of known classes.

These are the commands that I am using to generate the graph :

vcf="MCF7.manta.tumor.svs.hg38.vcf"

cov="MCF7.cov.corrected.bedgraph.txt"

jba $vcf \
$cov \
-n "${vcf%%.*}" \
--cores=32

and

gg = readRDS("jabba.gg.rds")

gg$meta 
gg$edges

gg$edges produces :

> head(gg$edges,2)
gEdge object with 2 edges
   sedge.id cn type CHROM POS paramRangeID  REF ALT QUAL FILTER IMPRECISE
1:        1  2  REF  <NA>  NA         <NA> <NA>       NA   <NA>        NA
2:        2  2  REF  <NA>  NA         <NA> <NA>       NA   <NA>        NA
   SVTYPE SVLEN END CIPOS CIEND CIGAR MATEID EVENT HOMLEN HOMSEQ SVINSLEN
1:   <NA>        NA                           <NA>
2:   <NA>        NA                           <NA>
   SVINSSEQ LEFT_SVINSSEQ RIGHT_SVINSSEQ BND_DEPTH MATE_BND_DEPTH mateid svtype
1:                                              NA             NA          <NA>
2:                                              NA             NA          <NA>
   first right coord mcoord mix MATECHROM MATEPOS tier like.indel edge.id class
1:    NA    NA  <NA>   <NA>  NA      <NA>      NA   NA         NA       1   REF
2:    NA    NA  <NA>   <NA>  NA      <NA>      NA   NA         NA       2   REF
   n1.side n2.side n1 n2
1:   right    left  1  2
2:   right    left  2  3

and no events are found (at lest simple events should have been listed) :

c = events(gg)

c$meta 

$simple
Null data.table (0 rows and 0 cols)

$amp
Null data.table (0 rows and 0 cols)

$chromothripsis
Null data.table (0 rows and 0 cols)

$chromoplexy
Null data.table (0 rows and 0 cols)

$tic
Null data.table (0 rows and 0 cols)

$events
Empty data.table (0 rows and 1 cols): ev.id

The R version is :

> R.Version()
$platform
[1] "x86_64-apple-darwin17.0"

$arch
[1] "x86_64"

$os
[1] "darwin17.0"

$system
[1] "x86_64, darwin17.0"

$status
[1] ""

$major
[1] "4"

$minor
[1] "2.2"

$year
[1] "2022"

$month
[1] "10"

$day
[1] "31"

$`svn rev`
[1] "83211"

$language
[1] "R"

$version.string
[1] "R version 4.2.2 (2022-10-31)"

$nickname
[1] "Innocent and Trusting"