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  1. 1. Usage
  2. 2. Details

1.  Usage

Function mut_sequence(chr, start, end) returns the mutated sequence between start and end on chromosome chr of the reference genome (primary reference genome unless parameter --build is used to specify an alternative reference genome). If end is unspecified, mut_sequence(chr, pos) returns the mutated allele at the specified location.

Simply put, function mut_sequence in

% vtools output variant chr pos 'mut_sequence(chr, pos)'

returns the alternative allele at the variant site for SNPs, - for deletion, and XXXR for insertion of XXX before reference allele R.

% vtools output variant chr pos 'mut_sequence(chr, pos, pos+5)'

returns the 5-base sequence at and after the variant sites with the variant for all variants in the master variant table.

Function mut_sequence will be identical to ref_sequence if the variant is outside of the specified region (e.g. different chr).

2.  Details

Examples: output mutated sequence around variants ▸

Let us get a test project

% vtools admin --load_snapshot vt_simple
Downloading snapshot vt_simple.tar.gz from online
INFO: Snapshot vt_simple has been loaded

It is not very useful but we can see the mutated sequence at the variant location,

% vtools output variant chr pos ref alt 'mut_sequence(chr, pos)' -l 10

1	4540 	G	A	A
1	5683 	G	T	T
1	5966 	T	G	G
1	6241 	T	C	C
1	9992 	C	T	T
1	9993 	G	A	A
1	10007	G	A	A
1	10098	G	A	A
1	14775	G	A	A
1	16862	A	G	G

It is more useful to see the context of the variants

% vtools output variant chr pos ref alt 'ref_sequence(chr, pos-1, pos+1)' 'mut_sequence(chr, pos-1, pos+1)' -l 10
1	4540 	G	A	GGA	GAA
1	5683 	G	T	TGC	TTC
1	5966 	T	G	GTG	GGG
1	6241 	T	C	ATG	ACG
1	9992 	C	T	GCG	GTG
1	9993 	G	A	CGG	CAG
1	10007	G	A	GGC	GAC
1	10098	G	A	CGA	CAA
1	14775	G	A	CGT	CAT
1	16862	A	G	GAA	GGA

Let us import some indels

% vtools init test -f
% vtools import SAMP3_complex_variants.vcf --build hg19
INFO: Importing variants from /Users/bpeng1/vtools/test/vcf/SAMP3_complex_variants.vcf (1/1)
SAMP3_complex_variants.vcf: 100% [=======================] 184 20.8K/s in 00:00:00
INFO: 135 new variants (1 SNVs, 77 insertions, 58 deletions, 7 complex variants) from 184 lines are imported.
Importing genotypes: 0 0.0/s in 00:00:00                                                                                                                                                                                                                                                            
Copying samples: 0 0.0/s in 00:00:00      

and check how the sequences are affected

% vtools output variant chr pos ref alt 'ref_sequence(chr, pos-1, pos+1)' 'mut_sequence(chr, pos-1, pos+1)' -l 10
1	10434	-  	C             	ACC	ACCC
1	10440	C  	-             	ACC	A-C
1	54788	C  	-             	TCC	T-C
1	54790	-  	T             	CTT	CTTT
1	63737	TAC	-             	CTA	C--
1	63738	ACT	CTA           	TAC	TCT
1	81963	-  	AA            	TAA	TAAAA
1	82134	-  	AAAAAAAAAAAAAA	CAA	CAAAAAAAAAAAAAAAA
1	82134	A  	-             	CAA	C-A
1	83119	A  	-             	CAA	C-A