Mapping quality value
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6.6 years ago
nuketbilgen ▴ 40

Hi,

I am new in the next generation analysis. I have 3 whole gene sequences.

I have several questions,

  1. How should I decide mapQuality filter value? Most of my reads has 60, but when I use  60 to filter my reads I lose approximately 3kb in one gene.  
  2. Is it possible to give different MapQ values for different chromosome with bamtools?  I am planning to use in one gene mapQuality">=20" and in the other two genes  mapQuality">=60".  

Thank you

 

 

next-gen bamtools filter gene mapQuality • 1.8k views
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What do you want to do? There's often no need to explicitly filter by MAPQ.

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Hi,

I want to generate a gvcf file (I have a pipeline ready for that). But when I use with mapQuality 60 filter I lose approximately 50 variation. 

After I get the gvcf file, haplotype determination in individual level and population level. I am working with cows :)

Thank you

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Fristly, 60 is an absurdly high quality to use for filtering, maybe 10 or so would be more useful (afterall, a MAPQ of 60 would bias against finding real variants, since any alignment showing a variant is more likely to have a lower MAPQ score). Secondly, some variant callers (e.g., GATK UnifiedGenotyper and samtools mpileup) will perform some filtering for you anyway.

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