how to "dope" a FASTQ file with known variants

Question

[win]

Hello, I need some positive control data i.e. NGS data in which I am aware which variants should be picked up, this is particularly true of pathological variants.

I read in the VAAST paper that doping is possible i.e. artificially(manually) introduce sequences that map to a variant and will be picked up during the pileup stage.

Any insights into how this could be done would be most useful.

Thanks in advance.

Answer 1

[morovatunc]

I have seen people used BamSurgeon in the article to create mutations to identify. You may give a try to this program and share your experience :).

BamSurgeon Git. https://github.com/adamewing/bamsurgeon

Article that I saw http://www.ncbi.nlm.nih.gov/pubmed/26381235

Answer 2

[WouterDeCoster]

An alternative that I've come across is to mutate the reference fasta you use to build an index for the mapping. As such you also simulate the mapping of reads containing mutants.