Changelogs » Amplimap



- add support for MIPGEN's `picked_mips.txt` file
- support MIPGEN probes with SNPs (probes `geneAex1_SNP_a` and `geneAex1_SNP_b` will be merged into a single probe called `geneAex1`)
- output a more detailed error message when no matching reads were found
- add tests


- Add support for custom aligners/variant callers
- Change default variant caller to GATK
- Add prefix option for Picard tools
- Fix crash if no variants found
- Add CircleCI for automated testing
- Add automated tests for variant merging, FGFR2/TLK2 tutorials


- Support running without annotation or with different sets of Annovar indices
- Dockerfile improvements
- Handle variant calls outside target regions
- Add pipeline diagram
- Add test for variant merging


- fix minor code warnings
- fix dependencies (require UMI-tools <1.0)
- add Dockerfile and update installation instructions


- improve error message when no reads with matching primers were found
- fix error when `use_raw_reads` is true and aligner is BWA


- updated documentation, add list of supported protocols
- renamed `tagged_bams_in` to `mapped_bams_in`
- added check to make sure only one input directory exists
- added check to confirm that `use_raw_reads` is set when using `unmapped_bams_in` or `mapped_bams_in`
- add link to cluster log documentation when showing error message
- internal changes:
+ made input rules conditional on input directory existing, to remove some ambiguity when input files are missing
+ make sure `stats_alignment` files are created even with `mapped_bams_in`
+ added test for multiple input directory check


- improved code documentation
- improved support for running the Snakefile stand-alone rather than through amplimap
- fixed naive mapping of untrimmed reads
- updated tutorials
- removed some deprecated code
- added `--latency-wait` parameter
- added new test cases


- fix version check for newer versions of picard tools
- add `requirements.txt` file
- internal changes:
+ add tests for config file reading
+ add test for UMI dedup
+ add/improve code documentation
+ refactor config file reading
+ stop recording versions for individual files
+ catch missing cythonized modules


- renamed output directories to match rule names:
+ `analysis/bam` -> `analysis/bams`
+ `analysis/bam/coverage` -> `analysis/bams/coverages`
+ `analysis/pileup` -> `analysis/pileups`
+ `analysis/pileup` -> `analysis/pileups`
+ `analysis/pileup_snps` -> `analysis/pileups_snps`
+ `analysis/umi_dedup` -> `analysis/bams_umi_dedup`
- added `general: umi_min_consensus_percentage` setting to specify the minimum fraction of reads in a UMI group that have to agree on the consensus
- add separate `pileups_snps` rule to only run SNP pileups
- improved check for missing paths
- fixed crash if config file was present but empty
- removed excessive logging in `stats_alignment` and `attach_tags_from_unmapped`
- improved documentation of config file


- added tutorials
- added rules to check that tools exist in path (and save their version) before trying to run them
- added check for valid coordinates in probe design file
- added check for non-overlapping target regions in targets file
- added support for space-separated SNPs file
- added `_fraction` columns to long pileups
- added config error checks
- added new tests:
+ run with BWA
+ handle UMIs
+ simulate variants
- fixed bugs:
+ error when mate names ended in /1 and /2
+ probe information missing from pileup files
+ fixed crash on errors with exon annotation file
- config changes:
+ added comments to default config to explain each option
+ added `general: use_raw_reads` option (should work with with unmapped bams as well as fastqs)
+ removed `no_probe_data` option (now detected through `use_raw_reads`)
+ moved some options from `general` into `parse_reads`:
* `trim_primers`
* `trim_min_length`
* `quality_trim_threshold`
* `quality_trim_phred_base`
+ changed defaults for `pileup:validate_probe_targets` and `pileup:filter_softclipped` to false
+ changed default variant caller back to Platypus