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6.0 years ago
vkgaur25
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30
I have a Illumina cancer panel data and after generating a bam file I want to find the total number of reads mapped to genome on some coordinates that I got from a bed file. I know that I can do that using samtools view while mentioning the exact position but I have 212 coordinates to look at and if I give a bed file mentioning 212 coordinates with bam file it would output a file containing reads and other details with coordinates but not total counts of reads in every single coordinate. How can I do that?