Recently published apps
We have just published and updated our Public Apps gallery with the BCFtools 1.15.1 toolkit – CWL1.2, containing the following tools:
- BCFtools Annotate – edits VCF files, adds or removes annotations.
- BCFtools Call – calls SNPs/indels (former “view”).
- BCFtools Cnv – calls Copy Number Variations.
- BCFtools Concat – concatenates VCF/BCF files from the same set of samples.
- BCFtools Consensus – creates consensus sequence by applying VCF variants.
- BCFtools Convert – converts VCF/BCF to other formats and back.
- BCFtools Csq – is a haplotype-aware consequence caller.
- BCFtools Filter – filters VCF/BCF files using fixed thresholds.
- BCFtools GTcheck – checks sample concordance, detects sample swaps and contamination.
- BCFtools Index – is used for indexing of VCF/BCF files.
- BCFtools Isec – creates intersections of VCF/BCF files.
- BCFtools Merge – merges VCF/BCF files from non-overlapping sample sets.
- BCFtools Mpileup – generates VCF or BCF containing genotype likelihoods for one or BCFtools multiple alignment files.
- BCFtools Norm – normalizes indels.
- BCFtools Query – transforms VCF/BCF into user-defined formats.
- BCFtools Reheader – modifies VCF/BCF header, changes sample names.
- BCFtools Roh – identifies runs of homo/auto-zygosity.
- BCFtools Sort – sorts VCF/BCF files.
- BCFtools Stats – produces VCF/BCF stats (former “vcfcheck”).
- BCFtools View – subsets, filters and converts VCF and BCF files.
We have also updated our Public Apps gallery with the following tools:
- VCFtools Vcf-sort 0.1.16, which sorts VCF files.
- Picard FixMateInformation 2.25.7, which verifies and fixes mate-pair information in a BAM file.