Full Changelog

Implemented enhancements:

• add needlestack logo in log.info #182
• add INFO field containing allelic frequency #174
• Add an option to only plot somatic mutations #149
• Make the main 3 processes pipe-friendly to avoid intermediate outputs #147
• Re-write pileup2baseindel.pl in C++ #146
• Flag possible cross-sample contamination of normal DNA in tumor samples #138
• Put ./. genotype when there is no power to identify a variant #137
• Implement Tumor-Normal pair somatic variant calling #133
• Add alignment plot in the PDF #73
• Make a script that would run needlestack without nextflow #72

Fixed bugs:

• max_dp default value in readme is wrong #176
• --help should exit 0 #161
• Manage bed specification for both bed and region #157
• Using renamed symlinks as input BAM files doesn't work with --use_file_name option #152

Closed issues:

• How to identify each sample? #166
• Github readme != Docker readme #159

Full Changelog

Implemented enhancements:

• Manage the three possible genotypes in vcf #130
• The graph showing AF vs log10(qval) should show phred-scaled qvalues #121
• Flag possible cross-sample contamination of normal DNA in tumor samples #138
• Put ./. genotype when there is no power to identify a variant #137
• Implement Tumor-Normal pair somatic variant calling #133

Fixed bugs:

• Contours seem to be incorrect #128
• correct file name extraction for sample name #126
• Let min_qval be equal to 0 #119
• plot improved error rate confidence interval #117

Closed issues:

• QUAL should not be reported as Inf in VCF when q-value=0 #125
• Add pipeline execution DAG in README #123

Full Changelog

Implemented enhancements:

• Change the number of entry in the INFO and FORMAT VCF fields #108
• Add contour lines for a set of qvalues in the plot #100
• color points by qvalues in regression plot #85
• Add an option to choose output VCF file name (--out_vcf?) #81
• Add an option to directly input a region for calling in the command line #71
• Change the way we publish new version #69
• Make the stable docker file more stable #68
• Add more tests in CircleCI #55
• Remove unnecessary intermediate outputs #51
• Improve the bed split method #47
• In the absence of a bed file the pipeline should run on the full reference genome #39
• Add version numbers in VCF output #20

Fixed bugs:

• VCF files have to be sorted #110
• Sometimes large number in VCF files are written in scientific notations #109
• error when coverage is null for every bam file #99
• Calling doesn't work when a region contains only T in the reference #96
• Check that BAM folder contains bam files #66
• Check if the gzi is present if the ref is gz #65
• Verify the user inputs are correct #42

Full Changelog

New features

• Added --no_indel option (#56)
• Added --out_folder option
• The software is now called needlestack (#31)
• Added program usage when launched with --help (#40)
• Added information about the pipeline in the log (#41)
• We now verify the user inputs are correct (#42)

Improvements

• Added a zoomed regression plot (#21)
• Added contigs in VCF header (#25 and #34)
• Moved to IARCbioinfo organisation repo (#22)
• Corrected typos in readme, help and log (#53)

Changes

• Option all_sites is now a flag called all_SNVs and no longer needs to be set to TRUE or FALSE (#33)
• Option do_plots is now a flag called --no_plots and no longer needs to be set to TRUE or FALSE
• Option sample_namesis now a flag called --use_file_name and no longer needs to be set to BAM or FILE

Bug fixes

• QVAL was wrongly called GQ for indels (#36)
• The pipeline no longer crashes if PDF files are not copied correctly (#49)

Testing/deployment bug fixes (don't affect users)

• CircleCI deploy.sh now triggers correctly Docker Hub (#26)
• Dockerfile now adds scripts from the correct branch (#27)

This pre-release has been deprecated and will no longer work with docker due to change of file names and repository names (see #22 and #31)

Compared to our even earlier internal version:

• Now we don't have a hard filter for strand bias by default (#15)
• Fixed a crash when no variant is found (#14)