manta-1.3.0

This is a major update from v1.2.2. It features improvements to candidate SV precision and genotyping accuracy, in addition to minor improvements in stability, runtime and error diagnostics.

Changed

• Change depth estimation read filter to better match the filter used for variant calling (MANTA-1296)
  • Expected depth per chromosome and local depth per locus/variant are now computed after removing filtered, pcr-duplicate, and secondary reads.
• Lower default memory requirements for scatter phase tasks (MANTA-1307)
  • Reduce from 2Gb to 1.5Gb to enable all cores by default on AWS c4.8xlarge/other c* servers.
  • Added new --callMemMb option to override this value for cases of extreme depth/chimera rate, etc
• Update htslib/samtools to 1.6 (MANTA-1331)
  • Updated from older 1.2 version to include improved checks on corrupted data.
  • Stopped vendoring zlib as part of this update, so zlib (w/ headers) is now a build requirement.
• Update the genotyping model (MANTA-1205)
  • Allow minor evidence of reference allele for hom-alt calls to tolerate a small number of noisy reads.
  • Filter out split reads with poor alignments to both alleles.
• Change the eligibility filter of split reads to only consider the most likely allele (MANTA-1332)
  • A split read is allowed to contribute to the split-read evidence if its alignment to the most like allele passes the eligibility filter.

Fixed

• Provide clear error message when attempting to configure/run with python3 (MANTA-1285)
• Improve error message/docs for alignment records with unknown sequence (SEQ='*') (MANTA-1295/[#111])
• Improve error message when two alignments use the same QNAME/read-number (MANTA-1293)
  • Message changed to help end-users track down the issue in the alignment file more easily - now includes chromosome name instead of contig index and 1-indexed alignment position.
• Fix CRC error from python gzip lib when generating evidence bam (MANTA-1270)
  • Remove the filter on evidence reads for SV candidates that are not in the file candidateSV.vcf.gz, because the file now contains all SV candidates without removing duplicates.
• Stop automatically clearing python environment variables (MANTA-1316)
  • This should allow python from certain module systems to be used, but may (rarely) cause instability due to conflicting content in a user's PYTHONPATH.
• Improve estimation of chimeric fragment rate (ie. fraction of reads which are split or in anomalous pairs) (MANTA-1261/[#103])
  • This fraction is used to set signal/noise thresholds important for somatic calling.
  • The secondary/supplemental segments of each split read are no longer counted as separate observations.
  • The method now accounts for many reads being classified as both anomalous and split.

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manta-1.3.0.centos6_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 6 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-1.3.0.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.