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pughlab / bamgineer

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
Apache License 2.0
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How to simulate homozygous deletion #11

Closed pcgen1 closed 5 years ago

pcgen1 commented 5 years ago

Hi suluxan, May I know the best way to simulate a homozygous deletion? Should the entry be mentioned (as stated below) in the cnv intereset bed:

chr1 123 124 0

pcgen1 commented 5 years ago

I meant: chr1 123 124 "empty string" 0

pcgen1 commented 5 years ago

sorry for mentioning very close stop , consider start to be 123 and stop to be 323 for example... :-).. Please let me know

suluxan commented 5 years ago

A lot of the updates to bamgineer v2 focused on user-specified alleles so the code was tailored towards specifying the haplotype. Homozygous deletions were already in the code but the input might fail in v2 since there is no associated haplotype code (i.e. AB). I will implement it as soon as possible and get back to you.

Thanks for your input!

pcgen1 commented 5 years ago

I just checked the results: my input trial (as mentioned) below to simulate homozygous deletions WORKED! chr1 123 124 AB 0

suluxan commented 5 years ago

Awesome! Yeah there are no restrictions to what your haplotype code would be as there should be no reads anyway! So AAAAA would work or any combination. Will fix this to make it more obvious and ability to put "NA" or something along those lines. Thanks!