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Mouse_Exome_Seq_VEP.sh
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Mouse_Exome_Seq_VEP.sh
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perl /data/mouse_exome_seq/Samples/DefaultProject/FASTQ/ensembl-vep/vep \
--input_file /data/mouse_exome_seq/Samples/DefaultProject/FASTQ/MMCID-26B_filtered_clean.vcf \
--output_file /data/mouse_exome_seq/Samples/DefaultProject/FASTQ/MMCID-26B_annotated.vcf \
--cache \
--vcf \
--dir_cache /home/bstansfield/.vep \
--species mus_musculus \
--assembly GRCm39 \
--refseq \
--force_overwrite \
--offline \
--fasta /home/bstansfield/.vep \
--everything \
--variant_class \
--show_ref_allele &
perl /data/mouse_exome_seq/Samples/DefaultProject/FASTQ/ensembl-vep/vep \
--input_file /data/mouse_exome_seq/Samples/DefaultProject/FASTQ/MMCID-30B_filtered_clean.vcf \
--output_file /data/mouse_exome_seq/Samples/DefaultProject/FASTQ/MMCID-30B_annotated.vcf \
--cache \
--vcf \
--dir_cache /home/bstansfield/.vep \
--species mus_musculus \
--assembly GRCm39 \
--refseq \
--offline \
--fasta /home/bstansfield/.vep \
--everything \
--variant_class \
--show_ref_allele &
perl /data/mouse_exome_seq/Samples/DefaultProject/FASTQ/ensembl-vep/vep \
--input_file /data/mouse_exome_seq/Samples/DefaultProject/FASTQ/TMCK1-14B_filtered_clean.vcf \
--output_file /data/mouse_exome_seq/Samples/DefaultProject/FASTQ/TMCK1-14B_annotated.vcf \
--cache \
--vcf \
--dir_cache /home/bstansfield/.vep \
--species mus_musculus \
--assembly GRCm39 \
--refseq \
--force_overwrite \
--offline \
--fasta /home/bstansfield/.vep \
--everything \
--variant_class \
--show_ref_allele &
perl /data/mouse_exome_seq/Samples/DefaultProject/FASTQ/ensembl-vep/vep \
--input_file /data/mouse_exome_seq/Samples/DefaultProject/FASTQ/TMCK1-23B_filtered_clean.vcf \
--output_file /data/mouse_exome_seq/Samples/DefaultProject/FASTQ/TMCK1-23B_annotated.vcf \
--cache \
--vcf \
--dir_cache /home/bstansfield/.vep \
--species mus_musculus \
--assembly GRCm39 \
--refseq \
--force_overwrite \
--offline \
--fasta /home/bstansfield/.vep \
--everything \
--variant_class \
--show_ref_allele &