Grouping mutations/Gene=f(sample)

GroupByGene is a small C++ tool grouping the data:

• CHROM
• POS
• REF
• GENE
• SAMPLE

by gene=f(sample). This tool is available on google code : http://code.google.com/p/variationtoolkit/source/browse/trunk/src/groupbygene.cpp
Example:

$ cat input.tsv

#CHROM	POS	REF	ALT	GENE	SAMPLE	
chr1	10	A	T	gene1	indi1
chr1	10	A	T	gene1	indi2
chr1	11	C	G	gene1	indi2
chr2	110	C	G	gene2	indi3
chr3	210	A	T	gene3	indi1
chr3	211	C	T	gene3	indi2
chr3	211	C	T	gene3	indi3
chr3	215	C	G	gene3	indi3
chr3	216	C	T	gene3	indi3
chr4	390	C	T	gene4	indi1
chr4	390	C	A	gene4	indi3

Calling "groupbygene:

$ groupbygene  --chrom 1 --pos 2 --ref 3 --alt 4 --sample 6 --gene 5 < input.tsv

GENE	CHROM	START	END	count SAMPLES	distinct MUTATIONS	count(indi1)	count(indi2)	count(indi3)
gene1	chr1	10	11	2	2	1	2	0
gene2	chr2	110	110	1	1	0	0	1
gene3	chr3	210	216	3	4	1	1	3
gene4	chr4	390	390	2	2	1	0	1

$ groupbygene  --chrom 1 --pos 2 --ref 3 --alt 4 --sample 6 --gene 5 --norefalt < input.tsv

GENE	CHROM	START	END	count SAMPLES	distinct MUTATIONS	count(indi1)	count(indi2)	count(indi3)
gene1	chr1	10	11	2	2	1	2	0
gene2	chr2	110	110	1	1	0	0	1
gene3	chr3	210	216	3	4	1	1	3
gene4	chr4	390	390	2	1	1	0	1

That's it,

Pierre