script-SV-genotyping

These are the scripts used for the project of ‘Assembly of a pan-genome for global cattle reveals missing sequence and novel structural variation, providing new insights into their diversity and evolution history’.

The description of workflow

The Deletion list needs to be constructed. We used the results of four software, retaining 50bp to 50 Mbp, at least two software-supported SV (overlapping 80%).
First, The result files generated by the four software programs was normalized to extract the breakpoint information of SV.
Then, integrate the results of multiple software, keeping SVs that are supported by at least two software and are 50bp to 5 Mbp in length. Extract all deletion breakpoints to get the deletion list.
Finally, using the bam files and the missing list file as input files, the obtained deletion joint genotyping with the GGDTRS.py script.

GGDTRS.py

The script joint genotype for the provided multiple BAM files according to the deletion list. The BAM file path list of each line is a BAM file path and a bed file containing deletion breakpoint was provided, the bed file that contains deletion breakpoints only needs to provide the chromosome numbers, START positions, and END positions.
In this script, the classification type of each DELETION site was detected for each BAM file. Finally, the detection results of multiple BAM files were merged to generate a VCF file.

Rely on third-party libraries

pysam (0.16.0.1); pandas (1.1.4); numpy (1.19.4)

optional arguments:

-h, --help show this help message and exit
-b, --bamfile_list List file of input BAM files. Must be indexed.
-l, --deletion_list Bed file of DELETION SV.
-o, --outfile Prefix for output filenames (same as the input BAM filename without the extension by default)
-t, --thread The number of thread(default=1).
-v, --version Show program's version number and exit