Finding difference in read depth between two BAM files

Question

[gtasource]

Hello,

I am looking to find the difference in read depth between two bam files (A, B.) My initial idea was to use Bedtools, find the total coverage of A and B, and then use Bedtools intersect to compare where they overlap and do not. However, I'm just curious if anybody has alternative suggestions or better software tools to use.

[GouthamAtla]

What data it is ? ChIP ? WGS ? RNA ?

Answer 1

[Pierre Lindenbaum]

using samtools mpileup and two bam files:

samtools mpileup -f ref.fasta in1.bam in2.bam | cut -f 1,2,4,7

1   101766  19  29
1   101767  19  30
1   101768  19  29
1   101769  123 188
1   101770  122 187
1   101771  122 189
1   101772  122 189

output is : chrom/pos/depth-bam1/depth-bam2

[Pierre Lindenbaum]

update:

samtools depth in1.bam in2.bam

Answer 2

[Hussain Ather]

There are a few methods....

• genomeCoverageBedtools
• samtools depth
• deeptools bamcoverage
• Rsamtools