Reads at position using samtools mpileup

Question

[charlotte]

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

[Pierre Lindenbaum]

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

[Matteo Schiavinato]

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. :)