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1. File Type
2. Detecting Headers
3. Extracting Records
4. Try It
Tell us about your file.
Custom File Type
Genomics File Type
How is it delimited?
Tab-delimited (TSV/TXT)
Comma-separated (CSV)
What's the structure of your file?
Flat file
Matrixed
Multi-value matrix
What type of genomics file?
VCF
Tell us about your file's headers.
My file has headers (and I don't need to change them)
Headers
Comma-separated list of headers.
My file has a "preamble" of non-header rows before the relevant content
How do we know what to skip?
Skip rows starting with a value until we reach one that does not
Skip rows until we reach one that starts with a value
Skip rows until we reach one that contains a value
Skip the first N rows
Value
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.
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.
X Column Name
What you want to call the entity described in the horizontally expanded columns, e.g. 'sample'
Value Name
What you want to call the value in the matrixed cells, e.g. 'frequency'
How should we handle compound-name columns?
How is the entity name separated from the value column name?
Underscore (_)
Space ( )
Dash (-)
None
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?
entity{delimiter}colname
colname{delimiter}entity
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"]
.
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