How to validate a bam file

Hello

I will cover on how to quick check our BAM file after mapping/alignment process.

In my case, I use BWA as for the mapping process of WGS data.

To validate our BAM file, first we need to install Picard tool, developed by Broad Institutes (https://broadinstitute.github.io/picard/). I will use Bioconda to install Picard

#quick check on bam file

$ conda create -n Picard python=3.7 $ conda activate Picard $ conda install -c bioconda picard $ picard -h $ ValidateSamFile -h #test one file $ picard ValidateSamFile I=/path/to/bam/file/SRR030257.bam MODE=SUMMARY #you can see warning or error on the terminal

Solution:

We must add Read Group information to our dataset using Picard utility before proceed with the next step.