... Hi, You can also explore BamTools toolkit with **"split"** option.
usage: bamtools [--help] COMMAND [ARGS]
Available bamtools commands:
convert Converts between BAM and a number of other formats
count Prints number of alignments in BAM file(s)
Can you paste the input data (few lines) which you are using as INPUT for GISTIC program? I would like to check the data structure to understand the problem.
You can follow the instructions on the given link :
Well explained with all the commands for SNP/INDEL calling using SAMtools.
: http://samtools.sourceforge.net/mpileup.shtml ...
You might be interested in knowing that **Windows 10 offers a new feature, A full, Ubuntu-based Bash shell that can run Linux software directly on Windows**.
There are different ways of representing data in a circular format (CIRCOS).
Go through the link mentioned above, here is one of the tutorials you can plot your CNV values with circos.