samtools view is not required before samtools sort (practical 4)

[yeban]

It is no longer required to pass SAM output from read mappers through samtools view -b. Instead, -o BAM can be specified directly to samtools sort.

[yannickwurm]

we should indeed implement these kinds of simplifications/updates On 2020Aug3, at 13:53, Anurag Priyam <notifications@github.com<mailto:notifications@github.com>> wrote: It is no longer required to pass SAM output from read mappers through samtools view -b. Instead, -o BAM can be specified directly to samtools sort. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fwurmlab%2Fgenomicscourse%2Fissues%2F62&data=02%7C01%7C%7Cfb16f818466a437deab708d837a3e929%7C569df091b01340e386eebd9cb9e25814%7C0%7C0%7C637320524414937821&sdata=1b%2FnLbpB6tyvIvrJIT3aGOVfYTaBCpWIUTP2weHHAxE%3D&reserved=0>, or unsubscribe<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAABEUYJU4OGEXNMH5WLAAI3R62QNPANCNFSM4PTIKU5A&data=02%7C01%7C%7Cfb16f818466a437deab708d837a3e929%7C569df091b01340e386eebd9cb9e25814%7C0%7C0%7C637320524414937821&sdata=Qwb3RJ6So5HtIKCV%2Fv1Gz1fj06ZFdDatk7VZZnZK%2FTA%3D&reserved=0>.