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annotate_csv.rst

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Annotating CSV Files

Sometimes, it is useful to annotate a whole CSV file where you have the chromosome, position, reference allele, and alternative allele in different columns. You can do this using the annotate-csv command of Jannovar.

You have to pass a path to a annotation database file and one or more chromosomal change specifiers. Jannovar will then return the effect, the HGVS annotation at the end of the line in the given CSV format and prints it out to the standard output.

Just imagine we have tab separated file with a header named input.tsv

contig  position    reference   alt
chr1    12345   C   A
chr1    12346   C   A

Now we run jannovar with this command an will get this output:

# java -jar jannovar-cli-.jar annotate-csv -d data/hg19_refseq.ser --input input.tsv -c 1 -p 2 -r 3 -a 4 --header --type TDF [...] contig position reference alt HGVS FunctionalClass chr1 12345 C A DDX11L1:NR_046018.2:n.354+118C>A: NON_CODING_TRANSCRIPT_INTRON_VARIANT chr1 12346 C A DDX11L1:NR_046018.2:n.354+119C>A: NON_CODING_TRANSCRIPT_INTRON_VARIANT

The format for the chromsomal change is as follows:

{CHROMOSOME}    {POSITION}  {REF}   {ALT}
CHROMOSOME

name of the chromosome or contig

POSITION

position of the first change base on the chromosome; in the case of insertions the first base after the insertion; the first base on the chromosome has position 1

REF

the reference bases

ALT

the alternative bases

Right now it is only possible to use teh column number and not the header column. This might be extendet in the future. Possible CSV file types are:

Default

Standard comma separated format, as for RFC4180 but allowing empty lines.

TDF

Tab-delimited format.

RFC4180

Comma separated format as defined by RFC4180.

Excel

Excel file format (using a comma as the value delimiter). Note that the actual value delimiter used by Excel is locale dependent, it might be necessary to customize this format to accommodate to your regional settings.

MySQL

Default MySQL format. This is a tab-delimited format with a LF character as the line separator. Values are not quoted and special characters are escaped with \. The default NULL string is \\N.