Used in: gor only

VARIANTS¶

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.

Usage¶

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

Options¶

`-gc`	Include this column (or columns) from the BAM file in the output.
`-readlength`	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
`-count`	Group by variant and add a column called `varCount` with the count. Equivalent to adding GROUP 1 -count -gc Ref,Alt \| RENAME allCount varCount

Examples¶

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