need to simulate inversion and translocation

[lmanchon]

--Hi,

i work on human genome and i want to know if it's possible to generate a Burkitt's lymphoma translocation (t(8;14)(q24;q32)): https://en.wikipedia.org/wiki/Burkitt%27s_lymphoma
and also an inversion such as the pericentric inversion of chromosome 9 (inv9) ?

thank you for your help.

[yjx1217]

Hi @lmanchon ,

As long as you can provide the genomic coordinates of these rearrangement breakpoints, then simuG can do the job accordingly. Note that for these cancer-related rearrangements, getting precise breakpoints could be tricky but a proximate one should be possible.

Best,
Jia-Xing

[lmanchon]

ok,
thank you for your feedback, can you tell me how can i configure these rearrangement breakpoints to use correctly your software.
For example if i want to configure one inversion on chr9 and a translocation between chr8 and chr14 ?
thank you --

[yjx1217]

Hi @lmanchon ，

The inversion and translation need to be defined in a VCF file with exact breakpoint coordinates specified according to the VCF specification of SV representation. Please see these examples in the README files. Please check the sample VCF files in the Testing_Example folder for details.

Simulate genome with pre-defined inversions specified in the input VCF file.

perl simuG.pl \
     -refseq ./Testing_Example/SGDref.R64-2-1.fa.gz \
     -inversion_vcf ./Testing_Example/sample.input.inversion.vcf.gz \
     -prefix output_prefix # the file name prefix for the output files

Simulate genome with pre-defined translocations specified in the input VCF file.

perl simuG.pl \
     -refseq ./Testing_Example/SGDref.R64-2-1.fa.gz \
     -translocation_vcf ./Testing_Example/sample.input.translocation.vcf.gz \
     -prefix output_prefix

Best,
Jia-Xing

[lmanchon]

--Hi,

thank you for your feedback.
The guidelines to structure the vcf file are not very clear, for example the position of the bracket in the syntax [chrI:194339[C
what the bracket means ?
If i want a translocation of 300 bases from human chr13 at position 28033909 (REF C) and chromosome 14 at a position chr14: 18516878 (REF C) how to configure that ?

thank you --

[yjx1217]

Hi @lmanchon ,

You can find detailed explanations on VCF's syntax for structural variants in this document https://samtools.github.io/hts-specs/VCFv4.5.pdf. See page 25-30.

Best,
Jia-Xing