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
Hello Mike, Please see responses below On 4/9/11 3:23 PM, Mike Dufault wrote:
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?
Yes, these are different analysis paths. Indel analysis is your query vs the reference you mapped against. SNP analysis is your query vs known variation (multiple public sources + the option to use your own variation data).
For SNP analysis, It seems that I need to filter on SAM, convert SAM-to-BAM, etc...
SNP analysis can use many different input formats - please see the tools in "SNP/WGA: Data; Filters" for the types accepted and more help.
For Indel, It seem that I should use the BWA output that is in SAM format for indel analysis.
Yes, start with a SAM file when using the tools in "NGS: 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.
The more specific you can be about the data, the better quality the results. Filtering would be recommended. Hopefully this helps! Apologies for the delay in reply, Best, Jen Galaxy team
Any thought, insight, etc. Thanks if advance, Mike
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Mike Dufault