whole genome and whole exome mapping

[wenluoParticipant]

Hi,
We are using novoalign for whole exome sequencing mapping for some time.
Now we start doing whole genome sequencing and we are going to use same tools for the sequence alignment.
But I’m wondering is there any difference between whole exome and genome data alignment in terms of parameters or other qc step?
Any suggestions are welcomed.
Thanks very much!
Wen

[Colin HercusKeymaster]

Hi Wen,

There shouldn’t be a significant difference. We usually get 95% mapped against WGS. Though there are a few small differences, WGS will have more multi-mapped reads so % of unique alignments will be lower. And, if you default to -r None option, mappings aren’t reported for multi-mapped reads the count of mapped reads by programs such as samtools flagstat will be less. You can add -r Random to get the counts up.

If you could send the novoalign log file from one each of a WGS and WES run I might be able to help further.

Kind Regards, Colin

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