fgbio

Tools for working with genomic and high throughput sequencing data

brewmacoslinux

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Tools for working with genomic and high throughput sequencing data

fgbio

Validate a SAM/BAM file for correctness$ fgbio ValidateSam --input file.bam --output validated.bam

Demultiplex reads by barcode sequences$ fgbio Demultiplex --input reads.bam --output demux.bam --read-structure +T +M +T

Group reads by molecular barcode for UMI deduplication$ fgbio GroupReadsByUmi --input reads.bam --output grouped.bam --strategy All