Hi!

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

thanks!