fgbio

Tools for working with genomic and high throughput sequencing data.

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RandomizeBam

Overview

Group: SAM/BAM

Randomizes the order of reads in a SAM or BAM file. Randomization is done by sorting on a hash of the queryname (and bases and quals if not query-grouping). By default reads with the same query name are grouped together in the output file; this can be turned off by specifying –query-group=false.

Arguments

Name Flag Type Description Required? Max # of Values Default Value(s)
input i PathToBam The input SAM or BAM file. Optional 1 /dev/stdin
output o PathToBam The output SAM or BAM file. Optional 1 /dev/stdout
seed s Int Random seed. Optional 1 42
query-group q Boolean Group together reads by queryname. Optional 1 true