Used in: gor only

VARJOIN

The VARJOIN command behaves similarly as a join with additional constraint that the columns denoting the reference and alternative allele are equal in both the left- and the right-source.

The command does join on single alleles, e.g. (ref,all), or multi-alleles (ref,a1,a2) or (ref,a1/a2). Also, the variations only have to be equivalent and not necessarily represented in the same manner, i.e. (chr1,2,’A’,’C’) and (chr1,1,’AA’,’AC’) are equivalent representations of the same variants.

The system can be configured to assume normalized variants. In that case, the varjoin defaults to -norm and -nonorm is needed for the dynamic normalization (-span relates to its function). If configured the other way around (like we do now) -norm skips the dynamic normalization on indels (the implementation is equivalent but faster than to apply varnorm first).

varjoin -nonorm == varnorm | join -snpsnp -xl ref,alt -xr ref,alt

varjoin -norm == join -snpsnp -xl ref,alt -xr ref,alt

Usage

gor ... | VARJOIN rightfile.gor [ attributes ]

Options

-ref col

The column denoting the reference seq. (for both left- and right-source).

-alt col

The column denoting the alternate (alleles) seq. (for both left- and right-source).

-refl col

The column denoting the reference seq. in left-source.

-altl col

The column denoting the alternate (alleles) seq. left-source.

-refr col

The column denoting the reference seq. right-source.

-altr col

The column denoting the alternate (alleles) seq. right-source. By default, ref and alt are in columns named Ref and Alt, Reference and Call or columns #3 and #4.

-as share

Defines the multi-allelic sharing threshold. If not specified single allele (alt) is assumed with a threshold of 1.

-xl cols

The columns to perform additional equi-join in the left-source.

-xr cols

The columns to perform additional equi-join in the right-source.

-xcis

Use case insensitive equi-join.

-maxseg size

The maximum ref segment size. Defaults to 1kb.

-l

Left-join style overlap, shows all rows in the left-source.

-n

Return only rows from leftfile.gor that do NOT overlap with rightfile.gor.

-i

Return only rows from leftfile.gor that are included in the overlap (without the columns from the right-source).

-ic

Return the rows in left-source and a column named overlap. Count which shows how many rows in right-source overlap.

-ir

Return the rows from right-source that overlap with the left-source. Depending on the nature of the left-source and the overlap condition, the join may have to be followed with SORT step to ensure GOR.

-rprefix name

A prefix to be added to the columns in the right-source.

-r

Reduced output. Do not include ref/reference and alt/call from the right source.

-s colname

Source column name (for GOR dictionary database file)

-e char

Character to denote empty field. Defaults to empty string, i.e. of length 0.

-p

Specifies the start and stop position

-span

Fuzz factor on the position, e.g. InDel variant normalization. Def. 1000bp, max 1Mb.

-norm

Assume left or right normalised variants, i.e. -span is zero. Skip dynamic normalization on indels. Equivalent to VARNORM, but faster.

-nonorm

Do NOT assume left or right normalised variants, i.e. ambiguity of InDels defined by -span size. Default join type -norm or -nonorm is set by Java system property ‘gor.varjointype’ or ‘varjointype’ in gor config file.

See also VARMERGE and the example for the LEFTWHERE command in relation to this.

The right-source can also be specified as a gor-stream, using the <(…) notation as in the JOIN command.