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Do I have to train a model for specific organism ? #200

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Modernism-01 opened this issue Jan 8, 2024 · 0 comments
Open

Do I have to train a model for specific organism ? #200

Modernism-01 opened this issue Jan 8, 2024 · 0 comments

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@Modernism-01
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Hi, Developers,

I was confused about the training model before I ran the PEPPER for variants calling. Could you tell me if I have to train a model for the pig before the SNP & INDEL calling? could I use the default arguments like this:

singularity exec --nv \
-B "${INPUT_DIR}:${INPUT_DIR}" \
-B "${OUTPUT_DIR}:${OUTPUT_DIR}" \
$IMAGE_PATH/pepper_deepvariant_r0.8-gpu.sif \
run_pepper_margin_deepvariant call_variant \
-b "${INPUT_DIR}/${BAM}" \
-f "${REF}" \
-o "${OUTPUT_DIR}" \
-p "${OUTPUT_PREFIX}" \
-t "${THREADS}" \
--ont_r9_guppy5_sup

Any suggestions will be appreciated.

Best,
Lingsen

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