[Samtools-help] Quality scores in a multi sample vcf file

[Keerthi S. <san...@uc...>]

Hi,

I am working with a merged bam file and using samtools mpileup followed by bcftools to do the variant calling.I am particularly interested in the SNP quality score reported in the vcf file.I see some SNP's are assigned a quality score of '999'.I am not sure how this quality score should be interpreted. Is there any threshold value after which the SNP's are assigned a quality score of '999'.

I usually consider a SNP quality score of 40 when working with single sample data.Any suggestions for quality cut-off  values I should be choosing when working with a merged bam? Thanks.