getting different value list from GATK gc content and CANOES

getting different value list from GATK gc content and CANOES

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I was trying to run codes from this paper

“A machine-learning approach for accurate detection of copy-number
variants from exome sequencing”

I need to get data from GATK GC content and CANOES and combined them, but I got a different value from each one,
GATK gave me gc.txt with 197921 line and CANOES gave 195841 lines so it couldn’t be combined.
why this happened and how could I get the same values?

P.S. I didn’t write anything, all I do was running their code, also I mailed them and waiting for their answers.
my reference gen is hg19.

the code is here.


CNV


GATK


CANOES

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