fgbio

Tools for working with genomic and high throughput sequencing data.

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AutoGenerateReadGroupsByName

Overview

Group: SAM/BAM

Adds read groups to a BAM file for a single sample by parsing the read names.

Will add one or more read groups by parsing the read names. The read names should be of the form:

<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<xpos>:<y-pos>

Each unique combination of <instrument>:<run number>:<flowcell ID>:<lane> will be its own read group. The ID of the read group will be an integer and the platform unit will be <flowcell-id>.<lane>.

The input is assumed to contain reads for one sample and library. Therefore, the sample and library must be given and will be applied to all read groups. Read groups will be replaced if present.

Two passes will be performed on the input: first to gather all the read groups, and second to write the output BAM file.

Arguments

Name Flag Type Description Required? Max # of Values Default Value(s)
input i PathToBam Input SAM or BAM file Required 1  
output o PathToBam Output SAM or BAM file Required 1  
sample s String The sample to insert into the read groups Required 1  
library l String The library to insert into the read groups Required 1  
sequencing-center   String The sequencing center from which the data originated Optional 1  
predicted-insert-size   Integer Predicted median insert size, to insert into the read groups Optional 1  
program-group   String Program group to insert into the read groups Optional 1  
platform-model   String Platform model to insert into the groups (free-form text providing further details of the platform/technology used) Optional 1  
description   String Description inserted into the read groups Optional 1  
run-date   Iso8601Date Date the run was produced (ISO 8601: YYYY-MM-DD ), to insert into the read groups Optional 1  
comments   String Comment(s) to include in the merged output file’s header. Optional Unlimited  
sort-order   SamOrder The sort order for the output sam/bam file. Optional 1