Sample reads across mapping
Hi everyone,
I have a mapping of PE reads to reference with a mean coverage of about 100 x. I need to sample (extract) reads across the alignment randomly to reduce coverage. Optimally but not necessarily, if there is heterozygote SNP, extract reads of both alleles.
Is there any way how to do it?
Thanks a lot in advance Milos
1 answer
see samtools view -s
-s FLOAT subsample reads (given INT.FRAC option value, 0.FRAC is the
fraction of templates/read pairs to keep; INT part sets seed)
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Pierre Lindenbaum
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