Question: Reads at position using samtools mpileup
0
gravatar for charlotte
2.8 years ago by
charlotte0
charlotte0 wrote:

Hi there,

I have a list of 386 cells and I am trying to find the number of reads at a specific position for each of them. I have done a samtools mpile up using the code below:

samtools mpileup -uf hs37d5.fa *.bam > results.bcf

How do I query my results.bcf to find out the number of reads at a specific position on chromosome 9? e.g. 9: 5073777-5073778?

I am struggling to figure out the documentation so any help would be appreciated

mpileup samtools • 1.6k views
ADD COMMENTlink written 2.8 years ago by charlotte0
1

I am struggling to figure out the documentation so any help would be appreciated

http://www.htslib.org/doc/samtools.html

samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam

ADD REPLYlink written 2.8 years ago by Pierre Lindenbaum129k
1

More general comment: we all struggled with that when it was our time, but careful and repeated reading of the link that Pierre has provided always got us out of the quicksand. :)

ADD REPLYlink written 2.8 years ago by Macspider3.0k
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