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High-depth filter for Mutect calls

akrishnaakrishna Member
edited December 2014 in Ask the GATK team


We are working on a cancer genome project and we use Mutect to call somatic mutations.
We have a question related to the high-coverage depth filtering. Below is a list of nearby positions output by Mutect
where the coverage in the tumor sample is very high but the coverage in the normal sample is not.

Partial output from *call_stats.out file -

contig position t_q20_count n_q20_count failure_reasons judgement

2 89849000 622 108 KEEP

2 89850117 508 152 KEEP

2 89850498 713 732 KEEP

2 89850649 583 403 KEEP

2 89850993 849 142 KEEP

2 89872002 540 286 KEEP

2 89877959 607 259 KEEP

These positions are not filtered out by Mutect.
I wonder why is a high-depth filter not used?
Would it make sense to filter these variants and which high-depth threshold should we choose?


Abhimanyu Krishna


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi there,

    Unfortunately, it is very difficult to give one-size-fits-all recommendations, and at this time we cannot give you detailed guidelines for further filtering. You will need to determine which filtering parameters are appropriate for your dataset. Good luck.

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