IntOGen-plus | Combination fails if gene has no symbol

[FedericaBrando]

While running latest version of IntOGen with updated regions, there was some weird behaviour with the combination. By digging a bit into the problem I found out the reason:

• Apparently some MANE transcripts are mapped to gene that do not have a name..yet. (i.e. ENSG00000269825 ) ; This leads to 2 main problem, one technical and one more conceptual:
• The technical one is just that it fails because the gene is seen as nan and therefore a float and not a str. (easy fix)
• The more conceptual is that, this means that whichever gene does not have a name will be counted as a hit, even if the genes are different, since we use as a main key, the gene name.
  • i.e. since we take the "Gene name" column, if we have multiple genes with no name, will consider them as the same leading to potential false positives.

I would say that there are two possible solutions here:

1. we get rid of this genes - easy, fast but might lose potential driver genes
2. we change identifier. we either chose the HGNC ID (univocal ID of digits - linked to a list of HUGO symbols, sinonyms to each other) or the ensembl ID for gene (ENSG),

[FedericaBrando]

awk -F'\t' 'BEGIN{OFS="\t"} $1 == "" {print NR, $0}' ../../28/d9938ac0b2c2a81d8788680a0d947b/PEDCBIOP_WXS_HGG_PRY.elements_results.txt
40              ENSG00000237378 Non Available   13   +  390     3       3       1  717  145.84077361972538      0.219   0.34138235294117647     0.28093709830345903     0.3760730408604518      0.2253515547073422        0.32280087566186855
494             ENSG00000187186 Non Available   9    -  264     0
495             ENSG00000188897 Non Available   16   -  9963    0
496             ENSG00000226690 Non Available   7    +  771     0
497             ENSG00000236543 Non Available   9    +  546     0
498             ENSG00000250803 Non Available   5    +  327     0
499             ENSG00000269825 Non Available   19   -  1926    0
500             ENSG00000282936 Non Available   17   -  3537    0
501             ENSG00000283205 Non Available   9    +  234     0
502             ENSG00000283536 Non Available   12   +  519     0

[FedericaBrando]

dirty solution for this run:

• manually change the oncodriveCLUSTL output that had the missing hugo symbol and rerun the seven cohorts.