I want to known how to use ssahasnp
Can you help me ?
My data :Illumina GA ,single-end reads
purpose:detect indel
Thank you very much

now, I have detected indels by ssahasnp, but there is a new problem,
how to parse the indels, the parse_indel runs unnormally.
Its output is "ERROR main:: reads group file" . I don't known the reason.
If you used it once, please tell me why.