This feature will be available in Goby 1.5+

Prerequisites

You must have an alignment compact file produced with Goby version 1.5+ (see how to produce such an alignment).

Display variations

You can display the sequence variations found in this alignment as follows:

java -Xmx2g -jar goby.jar -m display-sequence-variations goby-sample.entries

The command will produce the following output (clipped to the top 10 lines).

INFO  GobyDriver           - edu.cornell.med.icb.goby.modes.GobyDriver Implementation-Version: development (20100322162728)
Alignment contains 1 reference sequences
Loading the alignment goby-sample
206 chr1 102179690:38:A/G,102179697:31:C/T,
252 chr1 46473080:33:T/C,
328 chr1 52147593:7:A/G,
352 chr1 121138862:16:T/C,121138875:3:G/T,
372 chr1 51995117:5:T/C,51995141:29:G/A,
376 chr1 113777429:15:G/A,113777438:6:A/G,
432 chr1 144990111:29:A/T,144990122:40:A/T,

The display-sequence-variations mode also supports tab delimited format, and single base tab delimited format (see help for the –format option). The tab delimited format is shown below:

basename	query-index	target-id	position-on-reference	read-index	var-from	var-to	type
goby-sample	206	chr1	102179690	38	A	G	MUTATION
goby-sample	206	chr1	102179697	31	C	T	MUTATION
goby-sample	252	chr1	46473080	33	T	C	MUTATION
goby-sample	328	chr1	52147593	7	A	G	MUTATION
goby-sample	352	chr1	121138862	16	T	C	MUTATION
goby-sample	352	chr1	121138875	3	G	T	MUTATION

You can use the output option (-o) to specify the file where the data will be written. This will avoid interleaving console output message with the table of results.

java -Xmx2g -jar goby.jar -m display-sequence-variations goby-sample.entries -f tab_single_base -o out.tsv

Collect sequence variation statistics

The sequence-variation-stats mode helps create histograms of the frequency of sequence variations along the read length.

java -Xmx2g -jar goby.jar  goby-sample.entries -m sequence-variation-stats -o histogram.tsv

The resulting file will look like this:

query-index	count	count/total_variations	count/total_alignments
1	647	0.049416	0.016691
2	590	0.045062	0.015220
3	413	0.031544	0.010654
4	314	0.023982	0.008100