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Question: pileup --position in galaxy
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gravatar for mor.rub
14 months ago by
mor.rub • 0
mor.rub • 0 wrote:

How do I get samtools pileup to work only on a certain set of positions (say a BED file)?
position mpileup pileup samtools regions • 278 views
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modified 14 months ago by Jennifer Hillman Jackson ♦ 25k • written 14 months ago by mor.rub • 0
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gravatar for Jennifer Hillman Jackson
14 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k
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