<commit_before>.. image:: https://travis-ci.org/hammerlab/varlens.svg?branch=master
    :target: https://travis-ci.org/hammerlab/varlens

varlens
======================

A collection of Python tools for working with genomic variants and
next-generation sequencing reads. Not particularly fast for large datasets. The
emphasis is on exracting what you need from BAMs and VCFs into a CSV file for
further analysis.

Built on `varcode <https://github.com/hammerlab/varcode>`_ and `pysam <https://github.com/pysam-developers/pysam>`_.

varlens-variants
    Combine, annotate, and filter variants from VCF or CSV files. Available
    annotations include genes, variant effects, surrounding sequence context,
    counts of supporting reads from specified BAM files, and MHC I binding<commit_msg>Update README.rst<commit_after>.. image:: https://travis-ci.org/hammerlab/varlens.svg?branch=master
    :target: https://travis-ci.org/hammerlab/varlens

varlens
======================

A collection of Python tools for working with genomic variants and
next-generation sequencing reads. Not particularly fast for large datasets. The
emphasis is on extracting what you need from BAMs and VCFs into a CSV file for
further analysis.

Built on `varcode <https://github.com/hammerlab/varcode>`_ and `pysam <https://github.com/pysam-developers/pysam>`_.

varlens-variants
    Combine, annotate, and filter variants from VCF or CSV files. Available
    annotations include genes, variant effects, surrounding sequence context,
    counts of supporting reads from specified BAM files, and MHC I binding
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