Get read depth from Multiple bam files

Question

[ijlal.hyder2012]

Hello everyone,

I need some help, I have a Panel sequencing data (107 genes) from 18000 individuals, which is already aligned it to hg38 reference genome (1 bam file for each individual), As I have to merge this data with a WES data and I do not have the region information, I was just wondering if there is a way/tool to extract the regions from those 18000 bam files into a single file that can be further used to get those same regions out of the WES data.

I would really appreciate your help/suggestions.

Regards,

[GenoMax]

way/tool to extract the regions/depth from those 18000 bam files into a single file

For the entire genome? Take a look at mosdepth.

[ijlal.hyder2012]

Hi,

I actually wanted to get the regions out of those 18000 bam files into a single bed file based on that file I wanted to extract the exact same regions from WES data so that I can combine both data's and do the down stream analysis.

An example bed file can be found in the link below

wget -nd biobank.ndph.ox.ac.uk/showcase/showcase/auxdata/GRCh38_alt_mapping_noCHR.sorted.merged.bed

I was just wondering if it is possible to have something like this based on those 18000 bam files

Regards,

[Pierre Lindenbaum]

do you want the depth for each base of for each bed record ?.

[ATpoint]

If it is interval-wise then featureCounts can be a fast option. You will need to convert the BED file to a SAF like like

awk 'OFS="\t" {print $1"_"$2"_"$3, $1, $2, $3, "."}' in.bed > out.saf

and then count reads over these regions like

featureCounts -a out.saf -T ${Cores} -F SAF -o out.counts *.bam

For per-basepair use mosdepth as genomac suggested.

[enigmargs]

ATpoint Hi, I want to produce coverage plots for multiple .bam files together for a single .bed target file. I browsed through the mosdepth manual but couldn't find any direct commands to produce coverage plots across multiple samples. Do you suggest to use outputs from individual files in R software as shown in the blogpost here? Or are there any tools which produces such plots directly?

[GenoMax]

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