Implements method for calling genomic insertions from Long-Range Inverse PCR sequences as described in "Pradhan, Barun, et al. "Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing." Scientific reports 7.1 (2017): 1-12. https://www.nature.com/articles/s41598-017-15076-3
Dependencies for the software are python (2 or 3 series) and pysam
usage: LDI_PCR_call.py [-h] [-o OUTPUT] [-f FILTERED] -r REGION [-R REASONS]
[-V [VERBOSE]]
input
Implementing Long-Range Inverse PCR variant calling method for long read
sequencing (e.g. Oxford Nanopore) The overall strategy is: 10. Consider
supplementary alignments with mapping quality of at least 20 20. Discard all
reads that do not have an alignment in the user given primer region 30. Chain
supplementary alignments consequtive in both read and genomic coordinates with
approximately equal distances 40. Cluster the reads with compatible/similar
breakpoints and call the variants (i.e. breakpoints)
positional arguments:
input Input bam file for filtering reads [default:None]
optional arguments:
-h, --help show this help message and exit
-o OUTPUT, --output OUTPUT
Output bam for LDI-PCR reads [default:LDI_PCR.bam]
-f FILTERED, --filtered FILTERED
Output bam for discarded reads [default:None]
-r REGION, --region REGION
Region of the LDI-PCR primers required for mapping
[default:None]
-R REASONS, --reasons REASONS
For reads mapping to the target region, write read
names, filtering decisions and reasons to this file
[default:None]
-V [VERBOSE], --verbose [VERBOSE]
Be more verbose with output [and log to a file]
[default:False]