Can't simulate in human chromosome 13/14/15/22 and other two problems

[Former user]

Hi Charlie, There are three prblems. #1 I found there is nothing in .bam file when I simulate any variant in human chromosome 13/14/15/22. (show it in Attached figure1.PNG, figure2.PNG and figure3.PNG) I don't understand why. There is a bug or you design it like this on purpose? #2 And I couldn't make the simulation on chromosome Y and mtDNA because they both are haploid. Is there a solution to this problem? #3 What's more. I try a similar test as SVEngine / test / na12878 / test_na12878.sh. That is, I make a mixture sample, but I don't get an expected result when I test this mixture sample by featureCounts. DEL is normal counts as the mixing ratio. But what makes me confused is the result of DUP is similar to DEL, which shows the mixing ratio. However, the result of duplication should be different to the mixing ratio.(show it in attached figure4.PNG) #This is a exmaple for problem3 e.g. The mixing ratios are 0.5,0.75 and 1.0. The counts ratio of DUP for each sample should be 1.5,1.75 and 2, but the actual result is 0.5,0.75 and 2.

[Charlie Xia]

Hi,

are you referring to the given test data set or your own?

If the second, can you provide input files that I can try to reproduce and debug.

Given my time limits, you are always welcome to investigate the code by your own.

I am sure there will be bug somewhere, but in principle won’t be difficult to fix coz everything is python-level scripting.

Sorry for the awful slow reply and let me know if I can of more help.

‌

Charlie