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Tell us about your file.

Custom File Type Genomics File Type

How is it delimited?

What's the structure of your file?

Tell us about your file's headers.

My file has headers (and I don't need to change them)

My file has a "preamble" of non-header rows before the relevant content

What's the identifying information for a record?

Your file likely has many fields, but only a few that uniquely identify a record when looking for matches in another file. We call these "match keys", and use them as the basis for any match-based accuracy statistics.

Auto-populate Fields

Use the button below to automatically grab the header of your file (based on the previous steps) to configure your data model. Get columns from file

Configure Fields

Match Key Columns

List of columns that uniquely identify a record when looking for matches in another file. For example, 'chr,pos,ref,alt'.

Match Key Columns

Comma-separated list of columns that uniquely identify a record when looking for matches in another file. For example, 'chr,pos,ref,alt'.

If matrixed file, the x-column name will be automatically added to this.

How should we handle compound-name columns?

How is the entity name separated from the value column name?

Column header will be split into two by the first occurrence of this value.

In what order are the entity (x-column) and value-column names?

E.g. S1_VAF would be colname{delimiter}entity, where the sample is called S1 and the column is VAF.

Value Column Names

Comma-separated list of column suffixes (e.g. 'VAF,Dp' for columns like 'S1_VAF,S1_Dp,S2_VAF,S2_Dp' or 'VAF_S1,Dp_S1,VAF_S2,Dp_S2'. Please do not leave spaces between comma-separated items unless they are actually part of the suffix.

Should we explicitly include or exclude particular columns?

Get Columns

Comma-separated list of columns to be included

Skip Columns

Comma-separated list of columns to be skipped

Advanced

Filters

Filters are passed in an array and evaluated consecutively. They should reference column names in your parsed dataset and be prefixed by $ (e.g. "$vaf"). When comparing against strings, make sure to quote the left side of the expression in single quotes. For example: ["'$vaf' != 'NA'", "$vaf > 0"].

Check Results on Your File

Parse file

Advanced

Look good? Continue on to explore this and other files.

Comparison Files

Baseline

Drop a file here to use as the baseline sample.

Test

Drop a file here to use as the test sample.

Fill me up!

Drag and drop files from the Workspace Files panel on the left to the Baseline and Test buckets to auto-generate interactive reports.

Feeling lost? Check out our documentation.

Learn more

Workspace Files

Tiles
List

File Configuration

Settings apply to currently active baseline file.

Modify Columns

Set which columns are used for matching.

Modify Parser

Select or create a custom parser.

VCF Baseline.vcf

VCF Test.vcf

VCF Test2.vcf

Name	Send To	Parser
Baseline.vcf		VCF Pass-Only
Test.vcf		VCF Pass-Only
Test2.vcf		VCF Pass-Only

To add your own files here,

Widget Controls

Use these controls to customize your report.

Quick Reports

Quick Diffs

Absolute

Percentage

Show charts

Data Distributions

Chart grouping:

Overall Grouped

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