Overview¶
Jacquard is an open source suite of Python command line tools that provides a practical approach to integrating multiple patient samples and multiple variant callers. Jacquard is designed to be used by bioinformatic analysts; the output is intended to be useful to analysts and biological researchers. Both Jacquard and its documentation assume that users the basics of variant callers and VCF files. For more information about VCF files, see the Hts-specs.
Why would I use Jacquard?¶
Jacquard makes it easier to analyze multi-patient tumor-normal datasets especially when using multiple vairant callers.
Most variant callers have embraced the Variant Call Format (VCF) standard [r2], a file format which clearly and succinctly describes variants from one or more samples. However, while many callers follow the standard, they often adopt different ways to partition results (e.g. somatic file vs. germline file, or SNP vs. indel); likewise, each caller creates its own dialect of VCF fields and tags [r3] [r5] [r7].
Moreover, each variant caller follows its own algorithms, and produces different results for the same inputs. Because of this, it is valuable to run data through multiple variant callers and compare the outputs [r3] [r5] [r7]. However, since each caller has its own dialect, direct comparisons are difficult.
Jacquard transforms the dialects of different variant callers into a controlled vocabulary of tags with a consistent representation of values. Furthermore, it intelligently merges VCFs from different patients and callers to create a single, unified VCF across your dataset. The consistent tag names and represntations expedite downstream analysis; the intgrated VCF highlights both the prevelance of specific variants and the overall mutation loads across samples.
Jacquard normalized VCF dialects: Each variant caller records depth or alt frequency with a different tag name and representation. Jacquard translates format tags from different callers into a uniform set of tags.
Jacquard can merge or expand VCFs from any variant caller. Jacquard can translate depth, alt frequency, somatic status, and genotype tags from several somatic variant callers: