Count unique fragments from a given BAM file

Question

[Ankit]

Hi All, Could any one suggest a tool to count unique fragments from a given BAM file? My data is exome-seq

Any leads will be appreciated

Thanks

[Pierre Lindenbaum]

comment or validate your previous questions, please.

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[lieven.sterck]

Ankit :

do also take a minute to look at what Pierre Lindenbaum asked !

(that would be much appreciated ;-) , thanks )

[Ankit]

Sure I will look into.

Thanks

Answer 1

[lieven.sterck]

Does your BAM file contain UMI info or is it pure alignment?

here a few general pointers (for tools) : Picard MarkDuplicates ; sambamba markdup ; (samblaster?) . If the data contains UMI tags: have a look at the UMI_tools package

Also the BBtools package has subcommands to achieve this: clumpify.sh, bbduk.sh, ...

Those are mainly to make your data "unique" , for the counting part you can use samtools or alike

[Ankit]

Thanks, my data is non UMI for the counting part you can use samtools or alike

--counting unique fragments how? any flag /syntax?

[lieven.sterck]

the most basic one is :

samtools view -c <your bam file>

(will count everything, omitting you exome info )

a bit more 'advanced' : use bedtools coverage or samtools depth

(those you can 'subset' to only target your exome info)

[Ankit]

That wont count unique fragments. It will just count coverage

[Ankit]

No I got the logic make unique and count

[lieven.sterck]

exactly, first make unique and then count them :)

(don't think there is any that does this in one go)

Answer 2

[GenoMax]

a tool to count unique fragments from a given BAM file?

This can be a bit tricky. You can imagine a situation where you may have two fragments that may have some overlap but they could still be considered unique since they don't have identical sequence.

dedupebymapping.sh (https://bbmap.org/tools/dedupebymapping ) may also useful for using your existing BAM file (assuming the data is already mapped).

You could use a tool like clumpify.shfrom BBMap suite (https://bbmap.org/tools/clumpify ) to count reads and compress the file (read count is added to the fastq header) that are perfectly identical (and also allow for some mismatches). Other potential option is dedupe.sh (https://bbmap.org/tools/dedupe ).