Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

GATK HaplotypeCaller does not forward @PG BAM header lines to -bamout

Hey GATK Devs!

I'm using GATK (v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18) to call SNPs and Indels on a single sample. The reads were aligned with BWA (v0.7.12) and duplicates marked with Picard MarkDuplicates (v2.0.1). I run GATK HC to completion without issue (command-line parameters reported below); however, when I merge the -bamout output BAM files with samtools (v1.3.1), samtools issues the following warning:

[bam_translate] PG tag "MarkDuplicates" on read "HS1:152:C0HBWACXX:5:1202:17823:110576" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.

The output BAM files indeed lack any @PG lines in the headers, but preserve the PG:Z: tags on the reads. Is this intended?

The options to GATK I issued were:

-T HaplotypeCaller -R genome.fasta -L genome.00001.bed -mmq 25 -mbq 30 -ERC BP_RESOLUTION -I proper.srt.mdup.bam -o proper.00001.g.vcf.gz -bamout proper.00001.g.bam

Thanks!

Issue · Github
by Geraldine_VdAuwera

Issue Number
2106
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

Best Answers

Answers

Sign In or Register to comment.