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Hi
I have a question regarding the data from 1000 genome pilot3. I thought these data should have high coverage? But when I calculate the depth (number of reads on each site), there are 446,631,429 sites that are covered by at least one read for NA07048. The average depth is only ~3, and only 1.6% sites are covered by at least 8 reads. Does this sound right? Could anyone share some experience on this or point out what I did wrong here?
The 1000 genome file I used is
ftp://ftp-trace.ncbi.nih.gov/1000gen...33.2009_09.bam
I used the calDepth in the examples of samtools0.1.8.
Thanks much!
Cindy
I have a question regarding the data from 1000 genome pilot3. I thought these data should have high coverage? But when I calculate the depth (number of reads on each site), there are 446,631,429 sites that are covered by at least one read for NA07048. The average depth is only ~3, and only 1.6% sites are covered by at least 8 reads. Does this sound right? Could anyone share some experience on this or point out what I did wrong here?
The 1000 genome file I used is
ftp://ftp-trace.ncbi.nih.gov/1000gen...33.2009_09.bam
I used the calDepth in the examples of samtools0.1.8.
Thanks much!
Cindy
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