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manta-0.29.0
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@ctsa ctsa released this 28 Sep 18:19
· 686 commits to master since this release
v0.29.0
8a727a2

This release adds support for analyzing alignments in CRAM format. Sample alignments can now be provided in either BAM or CRAM (or combinations of these).

There are also two improvements to support the 1kg hg38 reference with decoy and HLA sequences: (1) improved job handling for thousands of small reference contigs and (2) improved support for contig names containing colons.

Full Changelog:

  • [#12]/MANTA-267 Support contig names with colons (for HLA contigs in 1kg hg38)
  • MANTA-252 Complete support for CRAM input
  • MANTA-264 Remove samtools from manta dependencies
  • MANTA-252 Change default chrom depth to median estimate from alignments
  • MANTA-263 Improve performance/stability for references with
    large numbers of small contigs
  • MANTA-261 Transfer stable components from Manta windows port

Prior WGS users note that the default method used to estimate chromosome sequence depth for the purpose of filtering high depth regions has changed to support CRAM: Manta now uses a median depth estimate from sampling chromosome regions instead of read counts from the BAM's index file. The new estimate is more robust, but may result in minor filtration differences compared to previous Manta versions.

Thanks to @jkbonfield for a key htslib edit (samtools/samtools#455) which enabled CRAM support to move forward, and @chapmanb for describing/patching the HLA contig name issue.

manta-0.29.0.centos5_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 5 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-0.29.0.release_src.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they are missing version numbers and build system changes to improve portability.

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