Reads at position using samtools mpileup
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
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charlotte •
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http://www.htslib.org/doc/samtools.html
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. :)