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How to install SAMTools and Gatk on CygWin and how to call it from Window`s Python and Java?

How to install SAMTools and Gatk on CygWin and how to call it from Window`s Python and Java?

samtools gatk cygwin
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written by flight22121 1

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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written by WouterDeCoster 4.8K

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

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written by russhh 575

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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written by Chun-Jie Liu 28

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