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How to check coverage in bam file?

Hi all,

How do I check the coverage of bam files? These files are bam files derived from GTEx rna short reads. For fastq files, you can count the number of lines and divide by 4 to get the reads wc -l / 4. Is there anyway to get read coverage from bam files similarly?

SRR1092349.bam                     
SRR1366519.bam      
SRR1455653.bam              
SRR820448.bam
bam
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updated by cmdcolin cmdcolin • written by shinyjj • shinyjj

2 answers

Read coverage can't be calculated by number of lines. You will need to use a program like pandepth (LINK) or modsepth (LINK) that can produce chromosome, specific interval or entire genome level estimates.

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written by GenoMax GenoMax

Is there way to get the overall coverage of one bam file instead of per chrmosome? Also would samtools fit for this?

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written by shinyjj • shinyjj

What have you tried? Please google "BAM coverage" and use one of the tools you find, or explore samtools depth and mosdepth. GenoMax has mentioned mosdepth for a reason - it is a lot faster than samtools.

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written by Ram Ram

pandepth provides coverage across the entire genome.

##RegionLength: NNNNNNNNNNN    CoveredSite: NNNNNNNNN  Coverage(%): 99.85      MeanDepth: 10.40
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written by GenoMax GenoMax 
$ samtools coverage -r chr11 in.bam
#rname  startpos  endpos  numreads  covbases  coverage  meandepth  meanbaseq  meanmapq
chr11    1         3302    358       3295      99.788    7.58237    17         60
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written by Pierre Lindenbaum Pierre Lindenbaum

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