Visualisation of read depth

Question

[AIMAR]

Hi all, I am currently on a genomic variants analysis and have completed the alignment step (BQSR and Apply , depth sequencing....). If any of you can help me or inform me about a way to visualize the reading depth (I have a targeted file BED.file) by plots. I don't know if you have an idea that could help me do this. I also ran samtools depth, mosdepth and pandepth. each generated sequencing depth results.

Thank you very much!

[Pierre Lindenbaum]

cross posted: https://bioinformatics.stackexchange.com/questions/23317/

[Pierre Lindenbaum]

to visualize the reading depth

what do you want to visualize ? min / max / median / in the capture / out of the capture / for each gene / etc// etc.. etc...

[AIMAR]

the mean of regions specified in the BED file

[GenoMax]

I also ran samtools depth, mosdepth and pandepth. each generated sequencing depth results.

Then plot the results in way you want.