Hi All,
 
I have a question about the NGS: Indel analysis and SNP Calling.
 
Assuming I have loaded my paired end reads, groomed, and  got all the way 
through to alignment with BWA my question the becomes does the analysis for 
indel analysis and SNP analysis split in the work flow?
 
For SNP analysis, It seems that I need to filter on SAM, convert SAM-to-BAM, 
etc...
 
For Indel, It seem that I should use the BWA output that is in SAM format for 
indel analysis.
 
Are these two above statments correct?
 
I also have a question regarding the input for indel analysis. Should I use 
the BWA output directly (which is in SAM format) or should I first "filter on 
SAM" and use that output (which is also in SAM format).  
 
I have tried the indel analysis using both filtered and unfilterd and I get 
very similar results. It seems to me that should use the "filtered on SAM" 
output where I can indicate that the reads are paired=Yes, proper pairs=yes, 
unmapped=NO.
 
Any thought, insight, etc.
 
Thanks if advance,
Mike
 
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