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0.4.0 - Soft-clipping, YAML and more
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@FelixKrueger FelixKrueger released this 29 Sep 09:51
· 101 commits to master since this release
0.4.0
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Learn about vigilant mode.

  • SNPsplit now supports soft-clipping of reads (CIGAR operation S).

  • SNPsplit now writes important statistics out in YAML format to enable easier integration into MultiQC. If tag2sort is called via SNPsplit itself, the ...sort.yaml file will be integrated into the main ...SNPsplit_report.yaml file (and deleted afterwards)

  • Added option --skip_tag2sort to allow the separation of the allele-tagging and allele-sorting (tag2sort) processes. This might be desired to add a de-duplication step such as markduplicates or deduplicate_bismark for Nextflow pipelines

  • For genomes that consist of chromosomes for which SNPs are recorded, and scaffolds for which there are no SNPs, now all chromosomes and scaffolds are printed to both the N-masked and full sequence genomes (see here).

  • Added auto-detection of single-end or paired-end files. This avoids accidentally processing paired-end files in single-end mode see here.

  • Now making use of variable genome_build instead of using GRCm38 invariably

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