Hello,
I'm working on human exome data (Illumina, pair-end), and I have consistently notice GSNAP produces at least 2-5 times more variants than BWA. While I'm sure not all of these extra predictions are false, I am concern most of these are false positives.
I've looked into the parameters for GSNAP and tried to tune them to restrict the # of variants I get. It would help a lot if anybody can share what parameters they use when running GSNAP on their NGS data, and what's their experience with it.
Thanks,
Casper
I'm working on human exome data (Illumina, pair-end), and I have consistently notice GSNAP produces at least 2-5 times more variants than BWA. While I'm sure not all of these extra predictions are false, I am concern most of these are false positives.
I've looked into the parameters for GSNAP and tried to tune them to restrict the # of variants I get. It would help a lot if anybody can share what parameters they use when running GSNAP on their NGS data, and what's their experience with it.
Thanks,
Casper
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