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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 -o proper.00001.g.vcf.gz -bamout proper.00001.g.bam


Issue · Github
by Geraldine_VdAuwera

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