sequencing reads simulation

[lyz1030]

Hi,



Can anyone explain the results of wgsim of me? What does the character 'R', 'M', 'Y' stands for in the third column? What is the meaning of the second column? In addition, if I have two haplotypes of a individual (with konwn heterozygous and homozygous variants), how can simulate the sequencing reads of this individual?



Thanks




20 62504 A R +

20 64077 A R +

20 64771 A M +

20 67086 C Y +

20 67502 G C -

20 68336 T G -

20 68678 A R +

20 70639 T Y +

20 70788 T W +

20 73011 T Y +

20 75088 T W +

20 76026 T W +

20 76306 C Y +

[simonandrews]

See this thread for an answer to your first question.

If you really wanted to simulate reads I guess you could do this by selecting a region around the SNP and making a mutated read from the reference genome. I guess the question would be why you would want to do this?

[ekg]

I have been using wgsim for some time in a testing context. However, I don't allow it to simulate reference-relative mutations. I do this with mutatrix, a population genome simulator which simultaneously simulates SNPs and indels. (Also, it generates VNTR indels based on sequence context). An example of the test setup is here: