Open Modernism-01 opened 8 months ago
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
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:
Any suggestions will be appreciated.
Best, Lingsen