which validate script you use?

bioinform / neusomatic

NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection

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which validate script you use? #66

Closed LeiHaoa closed 4 years ago

LeiHaoa commented 4 years ago

Hi, I wonder which validate script you use? I evaluated different validate methods like hap.py/som.py and just compare [chorm-pos-alt-ref]，this two functions showed different results. So, I am curious about which validate script you use to test detect results and truth file and get recall/precision??

Thanks!

msahraeian commented 4 years ago

Hi @LeiHaoa , I think hap.py can give you precision and recall. I usually use either hap.py or VarSim, which you can run it as:

python compare_vcf.py \
--regions EVAL_REGION.BED \
--out_dir OUT \
--reference REF.fa \
--true_vcf TRUTH.VCF \
--vcfs PREDICTION.VCF

LeiHaoa commented 4 years ago

thanks very much!