Release notes

Written By Divya Sain

DRS import from manifest file now available on the CGC

Expanding on the current feature that enables you to import DRS files by entering DRS URIs, we have now enabled DRS file import using manifest files containing all relevant information to import the files, along with associated metadata. This provides an easy and streamlined way to import a large number of DRS files from different sources such as Seven Bridges academic platforms or external sources.

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.

Divya Sain
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