Are there any human genome variant callers and BAM indexing and sorting tools to run on Windows 10? I run Pilon, but it asks to index and sort BAM. How to substitute SAMTools?
Nothing that is free comes to mind. You can always install linux subsystem for Windows 10 (for free) and do all you need to in a real bash shell on Win 10. There are three unix distros available now in Microsoft store. Choose ubuntu if you are new to unix.
Many Java based tools run on windows without issue. Picard tools is a Java version of samtools that runs on windows. You can also sort and index BAM files using the IGV GUI, or the igvtools command line.
well, there are two ways in windows 10:
Just to clarify for others reading this later. Bioconda only provides binaries for Linux and MacOS. Not Win10. Personally, I tried the WSL with Ubuntu and the VirtualBox approach. Both they both have old release and performance problems. You can install CygWin64 fairly easily in Win10, then struggle to add the developers packages for GCC and a few other needed packages (CygWin does not support apt-get or similar). Once done though you can easily compile the source release downloaded from htslib.org and similar. Very key is to make sure to do a ./configure before you do a make. So this was the best way to get Win10 executables available; with versions later than any other package manager. As Conda is good about keeping the latest release available, I sure wish they would add the Win10 binaries to their system since Conda supports it. If they did, I would take our Python project and move it to Conda in a heartbeat. Unfortunately, 90% of our users are on Win10 so ...
You can use Galaxy through a browser.
But there are very few people using Windows tools to do any of this, and even fewer who will be able to help you here. Use Cygwin if you don't have access to a dedicated Unix machine.
Wiping Windows or converting fully to linux isn't necessary. You can easily get the best of both worlds - just use the Linux subsystem for Windows. Way easier than dealing with VMs or cygwin and can utilize all of your computer's resources rather than dealing with a gimped linux VM. I've never had any issues getting anything to run on it (that I haven't also ran into on native linux distros).
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Why do you want to know that, just get Linux :)
option 1) install a linux virtual box https://www.virtualbox.org/
option 2) delete windows, install linux <=== BEST