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jayce_ocean 03-04-2011 12:40 AM

GATK calling Merged Bam files
Dear All,

can share your idea? i have tried to merge my bam files (bam file1, bam on) using samtools and picard. After then, i used GATK to call the SNP and refer to the merged bam file. However, the GATK always throw out genotyp results with 2 columns or more pertaining to my number of bam files prior the merging instead of a single column result for the merged bam file.

Any idea?anyone can share the experience?many thanks in advance...:)


jayce_ocean 03-04-2011 12:44 AM

i had done reheader and add the @RG tag referring to my merged bam file. But still, GATK always throw an error message stating the read error message or output each of every bam file results in each column prior the merging....any idea?i wanna results from GATK 1 column referring to the merged bam file results. thanks...

jayce_ocean 03-04-2011 01:07 AM

any trick?anyone have idea?or any settings in GATK i need to twist on?please help to share some idea or experience...thanks..

Jose Blanca 03-16-2011 01:15 AM

We usually merge bam files for GATK. Our code is exposed in a pipeline (, but if you like python you could use the underlying library (


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