How to generate alignment report from bam files
I am relatively new to the programs that analyze bam files. I am wondering if there is a program that allows us to have an alignment report of all the reads of a particular nucleotide from the bam file?
For example:
chr1:2876597
Total read: 130
A: 120
T: 0
G: 8
C: 0
N: 0
Del: 2
Ins: 0
I have over 200 bam files and I would like to have a report like above for all of them. Could anyone help? Thanks!
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Pierre Lindenbaum
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written
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kin182 •
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written
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kin182 •
2 answers
I've written : FindAllCoverageAtPosition http://lindenb.github.io/jvarkit/FindAllCoverageAtPosition.html
it reports the coverage+bases (not shown in the html doc)+cigar-operators at a given position for a set of files:
$ find ./ -type f -name "*.bam" |\
java -jar dist/findallcoverageatposition.jar -p "chr2:1234"
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Pierre Lindenbaum
That's essentially what samtools mpileup is doing, though I certainly hope you're not planning to actually write that out to a file.
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Devon Ryan
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If you decide a visual representation would be helpful, you can also use IGV; there is an automator script here that might make the task easier.