Question: BAM files after BWA MEM
1
gravatar for j.d.helix
2.3 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 • 1.4k views
ADD COMMENTlink modified 2.3 years ago by Bjoern Gruening4.8k • written 2.3 years ago by j.d.helix10
4
gravatar for Bjoern Gruening
2.3 years ago by
Bjoern Gruening4.8k
Germany
Bjoern Gruening4.8k 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 2.3 years ago by Bjoern Gruening4.8k

Hi Bjoern,

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

Ciao,

DHelix

ADD REPLYlink written 2.3 years ago by j.d.helix10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 100 users visited in the last hour