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aquaskyline / Clairvoyante

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

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TrainingModels and new Bam file

yangxiaofeill opened this issue · comments

commented

Dear authors,
Thanks for your Clairvoyante.
I try to use it as you described like:

cd training
python ../clairvoyante/callVarBam.py \
       --chkpnt_fn ../trainedModels/fullv3-illumina-novoalign-hg001+hg002-hg38/learningRate1e-3.epoch500 \
       --bam_fn ../testingData/chr21/chr21.bam \
       --ref_fn ../testingData/chr21/chr21.fa \
       --bed_fn ../testingData/chr21/chr21.bed \
       --call_fn chr21_calls.vcf \
       --ctgName chr21
less chr21_calls.vcf

I have downloaded the training data, however, I cannot find the trainedModels directory and also the trained model. Could you tell me where to download it or tell me how to train a model?

Another question, I want to run clairvoyante on a new BAM file, should I need to train a new model or what I need is just use your trained model?

Best
Xiaofei

commented

Dear authors,
Thanks for your Clairvoyante.
I try to use it as you described like:

cd training
python ../clairvoyante/callVarBam.py \
       --chkpnt_fn ../trainedModels/fullv3-illumina-novoalign-hg001+hg002-hg38/learningRate1e-3.epoch500 \
       --bam_fn ../testingData/chr21/chr21.bam \
       --ref_fn ../testingData/chr21/chr21.fa \
       --bed_fn ../testingData/chr21/chr21.bed \
       --call_fn chr21_calls.vcf \
       --ctgName chr21
less chr21_calls.vcf

I have downloaded the training data, however, I cannot find the trainedModels directory and also the trained model. Could you tell me where to download it or tell me how to train a model?

Another question, I want to run clairvoyante on a new BAM file, should I need to train a new model or what I need is just use your trained model?

Best
Xiaofei