Question: Cannot filer pileup result
0
gravatar for wangshu12
2.7 years ago by
wangshu120
wangshu120 wrote:

I did MPileup, and I want to filer the pileup result to find the information I needed. However, the software says " no pileup dataset available". After MPileup, the dataset format is VCF. It should be recognized by the  "Filter pileup" tool.

Please help me to solve this problem.

Thanks

Shu

samtools • 690 views
ADD COMMENTlink modified 2.7 years ago by Jennifer Hillman Jackson25k • written 2.7 years ago by wangshu120
1
gravatar for Jennifer Hillman Jackson
2.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

That particular tool uses pileup as a datatype input, not VCF

To obtain a pileup dataset, use the Mpileup or Generate pileup without the option genotype liklihood calculation. At the end of the run, the output will be in tabular format. Use the pencil icon to change the type to pileup and use the data with downstream tools, such as Filter Pileup.

To work with VCF datasets, see the tool group NGS: VCF Manipulation.

Details about all of these options are on the tool forms, both in the top option setting area and below in the help.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.7 years ago by Jennifer Hillman Jackson25k
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