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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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High quality reads determined? #2154

Closed jalalsiddiqui closed 5 months ago

jalalsiddiqui commented 5 months ago

When I run the variant caller, I get AD= high quality reads supporting a read and DP=raw read coverage.

The code I run is:

bcftools mpileup files/{filename}.bam \ -R ../vcf_ref/Homo_sapiens_assembly38.dbsnp138.common.noalt.vcf \ --fasta-ref ../ref_index/hg38.fasta.gz \ -a FORMAT/AD \ -Ou --threads {} | bcftools call -c -o files{filename}.sort.bam.mpileup.call.common.dbsnp.vcf --threads {}

Is there a cutoff for what is a high quality read and what is not?

Thanks,

Jalal

pd3 commented 5 months ago

Please check the usage and manual page of the program, there are various quality cutoffs applied. For example, entire reads are not excluded by default (--min-MQ) even when mapping quality is 0. However, there is a cutoff for minimum base quality (--min-BQ).