> Was that 2,000,000 reads pairs or reads? If it's read pairs, then probably 45,000 CPU seconds for a 30X WGS with 600 million read pairs. If we parallelize it over 10 CPUs, it will be less than 10 minutes. Not nothing though.
Yes, I think WGS samples can go way more than 1B reads depending on the coverage. Would it be possible to quickly check the first few lines of an input and its EOF like samtools quickcheck does as default?
Yes, I think WGS samples can go way more than 1B reads depending on the coverage. Would it be possible to quickly check the first few lines of an input and its EOF like
samtools quickcheckdoes as default?Originally posted by @tyamaguchi-ucla in https://github.com/uclahs-cds/package-PipeVal/issues/89#issuecomment-1837931403