I am looking at raw pindel output files and wondering if there is a way to change them into genotyped bed-type files. the main question is how does one genotype (decide if each individual does or doesn't have the structural variant) based on pindel's 6 number description per sample when one is using pindel on multiple samples. Would it be best to solve this problem by simply using pindel per individual?
The output would look something like :
*header* chromsosome start stop type size sample1 sample2 sample3 *SV1:* chr1 500 1000 del 500 1 1 0 *SV2:* chr1 1050 1100 del 500 0 1 0
the ones and zeros for each sample represent presence/absence of the CNV