index bam file command missing

alipirani88 / Comparative_Genomics

Micro 612 genomics workshop

http://comparative-genomics.readthedocs.io/en/latest/index.html#

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index bam file command missing #35

Closed zenalapp closed 6 years ago

zenalapp commented 6 years ago

For day 1 afternoon we sort the bam file but never index it. What's the command for indexing the bam file?

Around line 169

Is this the right command?

samtools index Rush_KPC_266__aln_sort.bam

I added this (lines 172 - 175), but please make sure it's right!

alipirani88 commented 6 years ago

We are indexing it after mark duplicates steps. Also i don't see your changes. May be try making a pull request when making any change so that we can keep record of the changes :)

zenalapp commented 6 years ago

Ohh, thanks!