BCFtools Mpileup Qual=0

Hi Galaxy Community members,
I mapped fastq.gz files with ref genome using BWA MEM and then used BCFtools mpileup to generate vcf file for downstream variant detection using varscan. When I look at this vcf file, the qual score is zero for all the location. Am i doing any mistake here? This also happened when i did samtools mpileup.
I will be grateful for all your suggestions.

Thanks
Sanjay

Hi Sanjay

There is not really enough information in your query to predict what is going on. I suggest that you might want to try out some of the workflows from the Galaxy training materials (e.g. the ones here: https://training.galaxyproject.org/training-material/topics/variant-analysis/) to test your approach against a well-known approach and see if you still get the same results.

Peter

1 Like

Hi Sanjay,
i have project, may you have good experince and more knowledge to advice me.
i have 3 accession number for raw reads for 3 whole genome,

Hi Dina_Yamin,
Can you please write in details abouth your project?
Thank you
Sanjay