Values -1 in mutation position

[FrancescoAlessandrini]

Hi!
Thanks a lot for you work on rnaseqmut, so useful!
I'm trying to find mutations from rnaseq data. When I obtain my mutation list from bam file, I find some mutation positions corrisponding to a cromosome but with the value "-1". I do not observe no "-1" in files generated from demo bam files. What does it means "-1"?
Thanks in advance,
Francesco

[NourMarzouka]

Similar observation, "-1" values as positions of some variants. Any idea of the reason?

Some selected example lines:
1 -1 C G 0 0 0 16
1 -1 C G 0 0 0 12
1 -1 G C 0 0 11 0

I noticed that when the position is "-1", the read numbers in the first two columns are always zeros.

[damisiak]

Dear all,

saw the same issue, any suggestions?

[damisiak]

Thanks for the update! Error is removed now.

[NourMarzouka]

Great! But what are these -1s? And if I already have some data with these -1s, then should I repeat the analysis?

[davidliwei]

Great! But what are these -1s? And if I already have some data with these -1s, then should I repeat the analysis?

You can safely ignore the lines with -1s as they come from the soft clipping of reads which are usually very few. The results will be slightly different using the latest code, but the majority of the results should be the same.