Question: Converting vcf to pileup
0
gravatar for sckinta
4.3 years ago by
sckinta550
United States
sckinta550 wrote:

I have vcf output from bayesfree and want to convert vcf output to pileup format which will be taken as input for popoolation2. Any script or software?

Thank you

freebayes popoolation2 pilup vcf • 2.4k views
ADD COMMENTlink modified 4.3 years ago by Nicola Casiraghi450 • written 4.3 years ago by sckinta550

VCF files won't typically contain all of the information required to generate a pileup of the original data. You'll need to do what Nicola Casiraghi wrote and simply make the pileup from the alignment files (assuming you have them).

ADD REPLYlink written 4.3 years ago by Devon Ryan91k
1
gravatar for Nicola Casiraghi
4.3 years ago by
Germany, Heidelberg, DKFZ EMBL
Nicola Casiraghi450 wrote:

Hi, you can perform pileup using samtools mpileup and specifying with option -l your positions of interest. 

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Nicola Casiraghi450

In other words, you'll need the BAM files....

ADD REPLYlink written 4.3 years ago by Sean Davis25k

Yes exactly, mandatory inputs.

ADD REPLYlink written 4.3 years ago by Nicola Casiraghi450
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