Summarize¶
The summarize command adds new INFO fields and FORMAT tags that combine variant data from the merged VCF. It will only work with VCF files that have been translated.
Summarizing Format Tags : The Jacquard-translated format tags from each caller are aggregated to create summary format tags.
Usage¶
$ jacquard summarize <input_file> <output_file>
positional arguments:
| input_file | Jacquard-merged VCF file (or any VCF with Jacquard tags; e.g.
JQ_SOM_MT)
|
| output_file | A single VCF file
|
Description¶
The summarize command uses the Jacquard-specific tags to aggregate caller information from the file, providing a summary-level view. Summary fields (e.g. average allele frequency) can highlight interesting variants.
The summarized format tags contain the prefix ‘JQ_SUMMARY’.
Example summary FORMAT tags¶
| Tag name | Description |
|---|---|
| JQ_SUMMARY_AF_AVERAGE | Average allele frequency across recognized variant
callers that reported frequency for this position
[average(JQ_*_AF)].
|
| JQ_SUMMARY_AF_RANGE | Max(allele frequency) - min (allele frequency)
across recognized callers.
|
| JQ_SUMMARY_HC_GT | High confidence consensus genotype (inferred from
JQ_*_GT and JQ_*_CALLER_PASSED). Majority rules;
ties go to the least unusual variant (0/1>0/2>1/1).
Variants which failed their filter are ignored.
|
| JQ_SUMMARY_SOM_COUNT | Count of recognized variant callers that reported
confident somatic call for this sample-position.
|
Refer to the summary VCF metaheaders for a full list of summary tags and descriptions.