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.

Marko Marinkovic