The scripts used for the project of ‘Assembly of a pan-genome for global cattle reveals missing sequence and novel structural variation
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 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