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).
% 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