Mutational context in results table

[jshleap]

Hello! I find this tool incredibly useful. Just one possible enhancement could be to report the upstream and downstream bases (context) of the mutation to make it easier to make mutational signatures ala Alexandrov et al. 2013 and to make figures suchs as figure 1 in Harris & Pritchard, 2017.

[dwinter]

Hi jshleap,

Thanks for filing this issue, it's definately a good idea and something I might work on if I can find time to dedicate to accumulate in the next little while.

In the mean time, I think you could do something similar with bedtools. If you run the example code in the README to produce an output file called test.out you can do something like this

bedtools slop -b 2 -g test.genome -i test.out | bedtools getfasta -fi test/data/test.fasta -bed -

>good_mutation:598-603
AACTA

Here test.gemome is a genome dictionary/sizes file with one row per record/contig in the reference

good_mutation	1200
indelish	1200
anc_het	1200
double_mutation	1200
qual_score	1200
std_bias	1200

Of course, doing it this way means you are assuming everything flanking the mutation has a reference allele (if we did in within accumulate we might be able to genotype the whole region and identify any non-reference / non-mutatoin alleles within the context too)