GISTIC from ASCAT

Question

[Hyper_Odin]

Hello everyone,

I am trying to run GISTIC from ASCAT segments, however,i am running into the following error.

1935 segment overlaps detected

I read somewhere that running bedtools merge would solve the problem, however I am not sure.

Is anyone doing the same ? or adopting any other methodology?

Thanks in advance!!

P

[Ram]

Can you show me the first 30 lines from the segmentation file you're passing as input to GISTIC please?

[Hyper_Odin]

Hi Ram, there you go

Sample  Chromosome      Start Position  End Position    Seg.CN
metastasis_H021-ARNHGQ0.47_6.segments_final.txt        1       762496  89447488        1.58496250072116
metastasis_H021-ARNHGQ0.47_6.segments_final.txt        1       89448360        249212481       1.8073549220576
metastasis_H021-ARNHGQ0.47_6.segments_final.txt        2       41369   169791765       1.58496250072116
metastasis_H021-ARNHGQ0.47_6.segments_final.txt        2       169791807       211336761       1.32192809488736
metastasis_H021-ARNHGQ0.47_6.segments_final.txt        2       211341050       242842587       2
metastasis_H021-ARNHGQ0.47_6.segments_final.txt        3       239347  73111973        1.58496250072116
metastasis_H021-ARNHGQ0.47_6.segments_final.txt        3       73111998        172538065       2
metastasis_H021-ARNHGQ0.47_6.segments_final.txt        3       172607274       197838366       2.32192809488736

[Hyper_Odin]

Sorry, this is how much I could paste, there is an error in the website while pasting more lines

[Ram]

You can use pastebin or GitHub gist to paste more lines, maybe you're being restricted because you're a new user. Did GISTIC give you something like line numbers when it reported the overlap? Take a look at this thread: GISTIC segment overlap error

If you got a line number as shown in the message in the other post, please extract those lines and show them to us.

[Hyper_Odin]

Hi, Ram thanks for the help...I figured out the issue. somehow I had duplicate files in the folder which caused the issue.

[Hyper_Odin]

Also, I would like to add that we cannot use ASCAT output for GISTIC input...since GISTIC expects all the chromosomes in the input file even if the chromosomes has normal ploidy.