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: