Question: pileup --position in galaxy
0
gravatar for mor.rub
10 weeks ago by
mor.rub0
mor.rub0 wrote:

How do I get samtools pileup to work only on a certain set of positions (say a BED file)?

ADD COMMENTlink modified 10 weeks ago by Jennifer Hillman Jackson23k • written 10 weeks ago by mor.rub0
0
gravatar for Jennifer Hillman Jackson
10 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

For Mpileup, look under Set advanced options > Select regions to call. The regions are defined by a BED format file in the history or you can just paste in the BED format coordinates.

For the earlier version of the tool, Generate pileup, filter the BAM input first as a distinct step. The tool BAM filter is one choice.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 10 weeks ago by Jennifer Hillman Jackson23k
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