Question: BAM files after BWA MEM
1
gravatar for j.d.helix
3.3 years ago by
j.d.helix10
United States
j.d.helix10 wrote:

Hi,

BWA-MEM in Galaxy produces a BAM file. Could anyone please tell me if the BAM file is sorted (by chromosome coordinates) and/or index?

I found NGS:SAMtools/Sort BAM file is able to do the sorting, but I don't know which tools in Galaxy can index a BAM file (similar to samtools index)...

Thank you very much in advance!

DHelix

bwa galaxy bam • 2.1k views
ADD COMMENTlink modified 3.3 years ago by Bjoern Gruening5.1k • written 3.3 years ago by j.d.helix10
4
gravatar for Bjoern Gruening
3.3 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi,

all BAM files are by default coordinate sorted and indexed in Galaxy. You don't need to deal with this as user :)

Ciao,

Bjoern

ADD COMMENTlink written 3.3 years ago by Bjoern Gruening5.1k

Hi Bjoern,

Thank you so much for your prompt reply! I understand.

Ciao,

DHelix

ADD REPLYlink written 3.3 years ago by j.d.helix10
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