Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Add large bam files to Galaxy bfantinatti Bioinformatics 19 11-24-2012 09:46 PM
picard add read groups HGENETIC Bioinformatics 0 01-25-2012 03:19 AM
best-practices for assigning read-groups for snp-caller brentp Bioinformatics 2 12-20-2011 07:34 AM
basic question about read groups efoss Bioinformatics 2 10-19-2011 04:32 PM
missing read groups for unaligned reads gfmgfm Bioinformatics 2 01-20-2011 05:49 AM

Thread Tools
Old 12-23-2012, 09:21 PM   #1
Junior Member
Location: India

Join Date: Sep 2012
Posts: 8
Default Add read groups in .bam file from 454 sequencing

how to add read groups in BAM file of 454 sequencing data using PICARD for further downstream processing in GATK?
Maulik23 is offline   Reply With Quote
Old 12-26-2012, 08:03 AM   #2
Location: Wisconsin

Join Date: Jun 2011
Posts: 87

I have never worked with 454 data, but I am still guessing that the BAM file would be similar to what you'll get for say HiSeq data. If that's the case, you could use the "AddOrReplaceReadGroups" module in picard tools to add read groups to your bam file. See the following link for more details:


java -jar AddOrReplaceReadGroups.jar INPUT=Input_file.bam OUTPUT=Read_group_added_file.bam RGID=ReadGroupID RGLB=ReadGroupLibrary RGPL=454Sequencing RGPU=PlatformUnit RGSM=Sample

I hope this helps.
aggp11 is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 11:58 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO