Question: GATK Mapping quality value
0
gravatar for Kritika
2.7 years ago by
Kritika260
India
Kritika260 wrote:

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

map quality gatk • 1.1k views
ADD COMMENTlink modified 2.7 years ago by Pierre Lindenbaum118k • written 2.7 years ago by Kritika260

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

ADD REPLYlink written 2.7 years ago by RamRS20k

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.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by genomax63k

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

ADD REPLYlink written 2.7 years ago by RamRS20k
0
gravatar for Pierre Lindenbaum
2.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:
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').

ADD COMMENTlink written 2.7 years ago by Pierre Lindenbaum118k

Also, from here: Gatk Multi-Sample Vcf Variantfiltration

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

ADD REPLYlink written 2.7 years ago by RamRS20k
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