False negatives in variant evaluation step
Answered
I have whole exome data from 6 subjects. I followed the GATK pipeline for preprocessing, then joint genotyped and hard filtered the variants using the default thresholds. I did variant evaluation using the truth dataset from genome in bottle database. I found more false negatives (sensitivity=40%) in my filtered vcf file. Because of low sample size,is this expected, more false negatives? Thanks
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Hi Priyadarshini Thirunavukkarasu,
I am going to move your post into our Community Discussions -> General Discussion topic, as the Germline topic is for reporting bugs and issues with GATK.
You can read more about our forum guidelines and the topics here: Forum Guidelines.
Best,
Genevieve
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Hi Priyadarshini Thirunavukkarasu,
When you say you are seeing more false negatives in this WES study, what are you comparing it to?
Thank you,
Genevieve
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I compared to the dataset (HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz) from Genome in bottle database
Is there way to check the pipeline which you are following to call and filter variants with an external dataset
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I see, yes I would expect that you would have more false negatives than the genome in a bottle truth set.
We have another filtering method you could try which can be run on a single sample, CNNScoreVariants. It might work out better than hard filtering, since you don't have enough samples for VQSR. I would recommend trying it out and seeing how the results compare to your hard filtering results.
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