xsamtools

xsamtools makes the samtools tooling from htslib and bcftools available through pypi packaging. These tools have been lightly modified to allow merges on VCF streams without an index.

Installation

pip install xsamtools

Installation requires a C toolchain. Typically Ubuntu/Debian systems should have the following packages installed:

• libbz2-dev
• liblzma-dev
• libcurl4-openssl-dev
• libncurses5-dev

libcurl4-openssl-dev may be omitted at the cost of some cloud support features in htslib.

Usage

After successful installation, the following executables are available:

samtools:

• htsfile
• bgzip
• tabix
• bcftools

xsamtools:

• merge_vcfs.py

xsamtools also provides Python tooling to create named (FIFO) pipes to Google Storage objects:

from xsamtools import pipes

reader = pipes.BlobReaderProcess("bucket-name", "read-key")
print("reader path", reader.filepath)  # local FIFO filepath

writer_key = pipes.BlobWriterProcess("bucket-name", "writ-key")
print("writer path", writer.filepath)  # local FIFO filepath

These streams appear as either readable or writable files on the filesystem. Such objects are not seekable.

A utility method is also provided to merge VCFs from GS objects:

from xsamtools import vcf

vcf.combine("src-bucket-name", ["first-src-vcf-key", "second-src-vcf-key"], "dst-bucket-name", "dst-vcf-key")

There is no formal limit on the number of VCF keys. Care should be taken that the VCF objects provided are aligned by chromosome or the merge will fail.

Docker

A Docker image with xsamtools installed is published at https://hub.docker.com/r/xbrianh/xsamtools