Questions about the output file about xtea HOT 3 CLOSED

Are you looking for germline/de novo pathogenic Alu insertions in the SMN1 gene? It may depends on the sample size I think. You can try with lower cutoff:

 The following cutoffs will be automatically set based on read depth (and also purity in the case of a tumor sample); 
 These parameters have been thoroughly tuned based on the use of benchmark data and also on a large cohort analysis. 
 For advanced users (optional major cutoffs):
 	--user: by default, this is turned off. If this option is set, then a user-specific cutoff will be used;
 	--nclip: minimum number of clipped reads;
 	--cr: minimum number of clipped reads whose mates map to repetitive regions;
 	--nd: minimum number of discordant pairs;

Also, there are different levels of output under the same folder as the vcf file. You may also check those ones.

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Thanks for your answer, I tried to lower the threshold to 1 and still did not find the Alu element in the SMN region. I even failed to find the relevant region in the original generated candidate_list_from_disc.txt or candidate_list_from_clip.txt file. Is it due to the homology of SMN1 and SMN2? You mentioned increasing the sample size, does it mean that I need to carry out case-control mode for detection? Or can multiple files be analyzed together?

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Well, that's not what I could know. How do you know there must be Alu insertions within SMN? Here, I only try to help to resolve technic issues for using xTea, not for research questions.

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