How to install SAMTools and Gatk on CygWin and how to call it from Window`s Python and Java?
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7.8 years ago
flight22121 ▴ 10

How to install SAMTools and Gatk on CygWin and how to call it from Window`s Python and Java?
samtools gatk cygwin • 2.8k views
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I don't know anything about cygwin (except that many people have trouble getting stuff working on it), but I do know that if you could get access to a Linux machine (server, virtual box, dual boot, standard installation) things would get far easier for you.

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Even though you set running environment well, you really want to use samtools or GATK to call big bam data on your Windows?

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Re samtools, just compile the source code. I haven't used GATK on cygwin

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