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[jumphone]

Hi, SPRINT has multiple types of thresholds for removing false positives, which might cause this issue.

One possible way to solve this problem:

Merge the RES lists of multiple samples, and then re-calculate the AD and DP.

For AD:

1. convert sam to zz (https://github.com/jumphone/SPRINT/blob/master/utilities/sam2zz.py)
2. calculate AD (https://github.com/jumphone/SPRINT/blob/master/utilities/getAlt.py)

For DP:
Use bedtools to calculate the coverage of each RES

Best,
Feng

[JieWu2012]

Hi Feng,

Thank you very much for the reply. It sounds like a good idea to re-calculate the AD and DP. Concerning the getAlt.py, is there any manual to explain what is the input and output? Besides, in the output of sprint from previous running, there is already a result file called "all_combined.zz". Do I still need to convert sam to zz?

[jumphone]

1. The output of getAlt.py is: CHR+'\t'+LOC+'\t'+TYP+'\t'+AD+'\n'
2. You can directly use the all_combined.zz.