v3.0.1 - Improved support and division of code

• ascat.R now pulled directly from ASCAT repository.
  • v2.4.3
• Add code to handle presence of chr on chromosomes automatically.
  • Chromosomes must be numeric (other than X/Y)
• Updated some docs.
• Failed detection of purity/ploidy now produces images files with 'No solution generated' for:
  • ASCATprofile.png
  • rawprofile.png

v3.0.0 - Update to core analysis

This release includes change to input files which make the legacy SnpGcCorrections.tsv et.al. incompatible. Please see the wiki pages for how you can build new versions.

Key points:

• Deprecated command line options
  • -snp_loci and -snp_pos are no longer required, warnings emitted if provided but continues to function (for now).
• Now generates segments on Y chromosome when appropriate.
• All required files generated from -snp_gc on the fly. Resulting analysis has a theoretically higher resolution (and number of SNPs ~doubled for GRCh37)

v2.0.1 - species agnostic, CRAM, parallel alleleCount

• Now species agnostic provided you can generate a panel of SNPs, approx 1 HET per 2kb is required. Tools are included in the package for guided and unguided SNP generation. More details can be found in the wiki.
• Supports CRAM
• Allele count phase is now threaded.

NOTE: Individual scripts called by ascat.pl have been renamed to prevent potential namespace clashes.

v1.7.2 - Correct output file name

This patch updated the *.samplestatistics.csv output file to be named *.samplestatistics.txt as the file is not csv (not tsv).

The format of the content has not been modified in anyway.

v1.5.2

Added . to the sanitise name code. Fixes issues with 'valid' sample names.

v1.5.1 - Revises gender determiniation to be based on normal sample only

Gender is considered XY on presence of any of the gender specific loci.

Only affects automatic gender determination, no changes to results for successfully processed data.

v1.5.0 - more robust gender testing

Now uses 4 Y chromosome specific loci to check gender. Default uses GRCh37d5, this can be overridden by supplying alternative loci file. The code is checking for coverage over these loci of >5 reads in >=50% of the provided loci.

v1.4.1 - Allow forced completion

It is now possible to have this complete even when ASCAT fails to find a solution. This is primarily in place to allow dependent processes to continue.

Adding -f results in a failed analysis reporting a normal contamination of 30%, tumour copynumber or 5/2 and normal copynumber of 2/1. These are the default values we use for CaVEMan when no copynumber is available.

Also fixes an issue in converting the raw copynumber output to VCF, please ensure that you update cgpVcf to at least version 1.2.2

ascatNgs-v1.4.0

Implementation now uses C version of alleleCounter script., ~50% faster.

Bugfix-v1.3.1

Error in deployment code, CN_to_VCF.pl now deployed correctly.