ad2vcf extracts allelic depth info from a SAM stream and adds it to a corresponding single-sample VCF file.
SAM input is read via stdin and the VCF input file is taken as a command-line argument. This allows expensive BAM/CRAM decoding to occur in-parallel using a pipe:
samtools view -@ 2 --input-fmt-option required_fields=0x218 \
../SRR6990379/NWD102903.b38.irc.v1.cram \
| ./ad2vcf file.vcfBoth SAM and VCF inputs must be sorted first by chromosome and then by read/call position.
The code is organized following basic object-oriented design principals, but implemented in C to minimize overhead and keep the source code accessible to scientists who don't have time to master the complexities of C++.
Structures are treated as classes, with accessor macros and mutator functions provided, so dependent applications and libraries need not access structure members directly. Since the C language cannot enforce this, it's up to application programmers to exercise self-discipline.
ad2vcf is written entirely in C and attempts to optimize CPU, memory, and disk access. It does not inhale large amounts of data into RAM, so memory use is trivial and it runs mostly from cache, making it very fast.
Processing a large CRAM file with human genome alignments against from the SRA project against dbGaP VCF data takes about 20 minutes on a modern workstation or server with ad2vcf averaging 4 to 5 MB (not GB) resident memory use. Memory use will spike briefly due to alignment buffering when processing regions where many alignments overlap multiple variant calls.
ad2vcf is intended to build cleanly in any POSIX environment on any CPU architecture. Please don't hesitate to open an issue if you encounter problems on any Unix-like system.
Primary development is done on FreeBSD with clang, but the code is frequently tested on Linux, MacOS, NetBSD, and OpenIndiana as well. MS Windows is not supported, unless using a POSIX environment such as Cygwin or Windows Subsystem for Linux.
The Makefile is designed to be friendly to package managers, such as Debian packages, FreeBSD ports, MacPorts, pkgsrc, etc. End users should install using a package manager. Note that pkgsrc can be used by anyone, on virtually any POSIX operating system, with or without administrator privileges..
I maintain a FreeBSD port and a pkgsrc package, which is sufficient to install cleanly on virtually any POSIX platform. If you would like to see a package in another package manager, please consider creating a package yourself. This will be one of the easiest packages in the collection and hence a good vehicle to learn how to create packages.
For an overview of available package managers, see the Repology website.
FreeBSD is a highly underrated platform for scientific computing, with over 2,000 scientific libraries and applications in the FreeBSD ports collection (of more than 30,000 total), modern clang compiler, fully-integrated ZFS filesystem, and renowned security, performance, and reliability. FreeBSD has a somewhat well-earned reputation for being difficult to set up and manage compared to user-friendly systems like Ubuntu. However, if you're a little bit Unix-savvy, you can very quickly set up a workstation, laptop, or VM using desktop-installer. GhostBSD offers an experience very similar to Ubuntu, but is built on FreeBSD rather than Debian Linux. GhostBSD packages lag behind FreeBSD ports slightly, but this is not generally an issue and there are workarounds.
To install the binary package on FreeBSD:
pkg install ad2vcfYou can just as easily build and install from source. This is useful for FreeBSD ports with special build options, for building with non-portable optimizations such as -march=native, and for work-in-progress ports, for which binary packages are not yet maintained.
cd /usr/ports/biology/ad2vcf && env CFLAGS='-march=native -O2' make install
cd /usr/ports/wip/ad2vcf && make installpkgsrc is a cross-platform package manager that works on any Unix-like platform. It is native to NetBSD and well-supported on Illumos, MacOS, RHEL/CentOS, and many other Linux distributions. Using pkgsrc does not require admin privileges. You can install a pkgsrc tree in any directory to which you have write access and easily install any of the nearly 20,000 packages in the collection.
The auto-pkgsrc-setup script will help you install pkgsrc in about 10 minutes. Just download it and run
sh auto-pkgsrc-setupThen, assuming you selected current packages and the default prefix
source ~/Pkgsrc/pkg/etc/pkgsrc.sh # Or pkgsrc.csh for csh or tcsh
cd ~/Pkgsrc/pkgsrc/biology/ad2vcf
sbmake install clean clean-dependsSee the pkgsrc documentation for more information.
Community support for pkgsrc is available through the pkgsrc-users mailing list.
Packages for libxtend are known to exist in the following package managers. These are maintained by third parties and not directly supported here.
If you would like to add this project to another package manager rather than use FreeBSD ports or pkgsrc, basic manual build instructions for package can be found here. Your contribution is greatly appreciated!