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Releases: ICGC-TCGA-PanCancer/PCAP-core

v2.1.0 - xam_coverage_bins.pl

01 Apr 14:02
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Pre-release
  • Adds xam_coverage_bins.pl which calculates fraction of targets covered at various depths (BAM/CRAM), using BED/GFF3 as target bait file.

warning please ensure all of your downstream tools will function without legacy samtools.

v2.0.1 - CRAM, samtools 1.3+, htslib

29 Mar 14:57
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Pre-release
  • bwa_mem.pl
    • allow user to specify BWA mapping parameters
    • now accepts CRAM as input
  • bamToBw.pl - now accepts CRAM as input.
  • bam_stats - Adds 2 new stats:
    • #_mapped_pairs
    • #_inter_chr_pairs
  • Dependancy changes
    • WARNING: ensure all related tools handle these updates
    • samtools, now only uses htslib based versions (1.3+, handling deprecated use of sort)
    • Bio::DB::HTS htslib bindings replacing Bio::DB::Sam

v1.14.0 - Adds ability to disable duplicate marking

15 Mar 11:49
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bwa_mem.pl:

  • new option -nomarkdup allows generation of BAMs without running duplicate removal
    • For some types of quantitive targeted/amplicon analysis this is necessary.
  • deprecated option -charts - has been non funtional since switch to bam_stats from bam_stats.pl
    • Still possible to generate with bam_stats.pl (if this is imperative to your use case please let us know)

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bam_stats unit tests

23 Feb 16:35
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  • unit tests added for bam_stats c
  • bugfix to median inset size calculation

Additional features in perl modules and improved bam_stats

04 Feb 10:46
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Improved bam_stats memory handling.
bam_stats now exits when '-v' requested rather than waiting for stdin.
bam_stats version is now dependant on perl module version to prevent mis-match due to having it in multiple places.
Added additional options to sample_name parsing from BAM.

v1.11.0 - Minor changes to functionallity (all backwards compat)

11 Jan 12:56
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1.11.0

  • bam_stats - new rna switch to give more appropriate insert size stats
  • bam_stats - more robust handling of optional RG header entries
  • bam_stats - allows streaming IO (thanks to @jenniferliddle)
  • bwa_mem.pl - Handle ' in RG header line/IDs
  • Generally improved version handling and updated versions of some tools.

v1.10.0 - Additional download features

24 Aug 10:50
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Adds DKFZ, Broad to results downloads
Slightly more robust GNOS handling
Minor fix to BWA-mem wrapper to work better with links

v1.9.4 - bwa_mem.pl handles single end sequencing appropriately

17 Aug 12:05
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This means relevant data is skipped and for filed containing only single ended sequencing an error is thrown.

Also updates cpanm location.

v1.9.1 - change log locations

05 Aug 12:08
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Changed final location of logs generated by bwa_mem.pl and bwa_aln.pl so that multiple analysis in same output location is safe.

v1.9.0 - enhanced BWA-mem mapping

03 Aug 12:21
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Now possible to start from merged BAM files with multiple read-groups.

Also fixes #52 and #53.