Question: what is the ”indel pileup file“ needed for somaticsniper fpfilter
1
gravatar for heartheone
3.4 years ago by
heartheone70
China
heartheone70 wrote:

The manual says " Before proceeding you will need to obtain and compile bam-readcount (https://github.com/genome/bam-readcount). You will also need to generate a samtools pileup (not mpileup) indel file."

I wonder how could I get a indel pileup file?

just simply  use samtools to convert normal/tumor bam?

samtools pileup -f $reference $normal_bam

 

Thanks!Wei

tool somaticsniper next-gen • 1.1k views
ADD COMMENTlink modified 3.4 years ago by ernfrid380 • written 3.4 years ago by heartheone70
0
gravatar for ernfrid
3.4 years ago by
ernfrid380
Saint Louis
ernfrid380 wrote:

You should use the tumor BAM and run samtools pileup as so:

samtools pileup -cvi -f $reference $tumor_bam > $indel_pileup_file

ADD COMMENTlink written 3.4 years ago by ernfrid380
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