Perbase base-depth

Question

[S.O.T.AL-HASHIMI2]

Hi all, I hope everyone is doing great. may I ask if anyone knows how can I get perbase base-depth function? I have followed the instruction in https://github.com/sstadick/perbase and downloaded it by conda install -c bioconda perbase. The help function shows that only simple-depth function is included and it doesn't support lots of options like selecting specific region or filtering according to the base quality and I need these for my analysis.

Ps: I need to quantify mismatches like A-G or T-C mismatches. an example of the output of perbase base-depth is below

and that is why I'm interested specifically in perbase. your help is much appreciated.

Best regards, Surar.

[cpad0112]

IGVtools gives per base depth at any given position (from bam files).

Answer 1

[S.O.T.AL-HASHIMI2]

Hi all, I would like to share the solution if anybody has the same issue. the problem was I had installed an old version of perbase and all I needed was to reinstall the tool using conda install -c bioconda perbase=0.8.1 and now I have all the functions required. Thanks Surar

Answer 2

[Pierre Lindenbaum]

samtools depth -r 'chr1:234-456' -q 78 in.bam

[S.O.T.AL-HASHIMI2]

Thank you very much for your reply, I'm not interested in simple depth but I need to quantify mismatches. I have edited the question too.

[Pierre Lindenbaum]

see also sam2tsv: http://lindenb.github.io/jvarkit/Sam2Tsv.html

[cpad0112]

Another way is to subset bam based on your requirements and pass that bam to perbase app.

[S.O.T.AL-HASHIMI2]

Thanks cpad0112, is there any tools that filter according to single base quality from bam? because I need to exclude the low quality and N bases before the analysis.

[cpad0112]

try sambamba and filter syntax and parameters is here: https://github.com/biod/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax. Base quality filtering should have been done at fastq instead at bam level. At this point, most of the filters work at mapping quality.