running time · 7ce9c17494 - Choppy for Reproducible Omics Pipeline

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LUYAO REN 6 年前

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															  --algo RNASplitReadsAtJunction --reassign_mapq 255:60 SPLIT_BAM
															
															  --algo RNASplitReadsAtJunction --reassign_mapq 255:60 SPLIT_BAM
														
															```
															
															```
														
															**(5) Base quality score recalibration **
															
															**(5) Base quality score recalibration**
														
															```bash
															
															```bash
														
															sentieon driver -r $fasta -t $nt -i SPLIT_BAM --algo QualCal -k $dbsnp -k $known_Mills_indels -k $known_1000G_indels recal_data.table
															
															sentieon driver -r $fasta -t $nt -i SPLIT_BAM --algo QualCal -k $dbsnp -k $known_Mills_indels -k $known_1000G_indels recal_data.table