Perl Script: Use Mpileup'Result To Find A Region'S Deletion

Question

[siyu]

how to write a perl script that uses the mpileup'result to find a genomic region's deletion？？is there anyone haveing this problem?? thanks!

Answer 1

[Michael]

It is not possible to prove deletion larger than the average read length from e.g. observing a coverage of 0 in a given location, because the lack of coverage might be due to random factors, in case you had that in mind. If you use samtools mpileup, and do not turn indel calling off (e.g. with -I), then indels should be called and be contained in the VCF file. A short deletion can be identified in the ALT column, e.g. as described here or simply by comparing the ALT and REF column.

[siyu]

Thanks for your answer ! I actually want to use breakdancer's (a tool to detect structural variants) result as the region , and use the mpileup's to refine the large deletion' breakpoint.So is there any problem?