Used in: gor only


The VARIANTS command returns the variants found in sequence reads and their associated quality. The variant quality is simply the base-quality of the first position in the variant.


gor file.bam | VARIANTS [-gc cols] [-readlength size (def 1000bp)] [-bpmergedist bpsize (def 3)]



Include this column (or columns) from the BAM file in the output.


The max read length. Defaults to 1000 basepairs if none is specified.

-bpmergedist bpsize

If larger than 0 then the variants command will also return merged phased variation, i.e. it will in addition to the basic varations return merge variations for variations within the given merge distance


Group by variant and add a column called varCount with the count. Equivalent to adding GROUP 1 -count -gc Ref,Alt | RENAME allCount varCount


gor file.bam | BAMFLAG -v | VARIANTS -gc firstInPair | GROUP 1 -gc ref,alt -count -min -max -ic firstInpair
| WHERE allcount > 2 AND min_firstInPair = 0 AND max_firstInPair = 1