Question: Indel Work Flow Questions
0
Mike Dufault • 270 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?
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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modified 7.6 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
7.6 years ago by
Mike Dufault • 270
