GATK Mapping quality value

Question

[Kritika]

Hi all, can any one explain me MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1) this quality filter . And why (1.0 * DP ) dp multiplied by 1.0

[Ram]

Where did you find that quality filter? Also, please add more details to your question and write in coherent language.

[GenoMax]

Option -filter "MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" filters out variants for which reads with zero mapping quality constitute more than 10% of all reads at this site. Variants filtered out with this criterion will be labeled as HARD_TO_VALIDATE in the filtered VCF file.

From GATK best practices variant guide v.2 that seems to have been retired but is referred to here.

[Ram]

Ah, I see. Thank you - but I still feel that OP should have included that information in the question.

Answer 1

[Pierre Lindenbaum]

if( "Count of all reads with MAPQ = 0 across all samples" > 4 AND (( "Count of all reads with MAPQ = 0 across all samples" / "DEPTH as double")  > 0.1)

"1.0 * " because 'DP' is an integer an we need a floating-number when dividing another integer (else the result of the above division would always be '0').

[Ram]

Also, from here: Gatk Multi-Sample Vcf Variantfiltration

all of the samples combined in total have less than 5 reads for the SNP