GATK calling Merged Bam files

jayce_ocean · 03-04-2011, 12:40 AM

Dear All,

can share your idea? i have tried to merge my bam files (bam file1, bam file2...so 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...

Regards
Jayce

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 (http://bioinf.comav.upv.es/ngs_backbone/), but if you like python you could use the underlying library (https://github.com/JoseBlanca/franklin).

Regards.

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03-04-2011, 12:40 AM	#1
jayce_ocean Junior Member Location: location Join Date: Sep 2010 Posts: 5	GATK calling Merged Bam files Dear All, can share your idea? i have tried to merge my bam files (bam file1, bam file2...so 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... Regards Jayce

03-04-2011, 12:44 AM	#2
jayce_ocean Junior Member Location: location Join Date: Sep 2010 Posts: 5	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...

03-04-2011, 01:07 AM	#3
jayce_ocean Junior Member Location: location Join Date: Sep 2010 Posts: 5	any trick?anyone have idea?or any settings in GATK i need to twist on?please help to share some idea or experience...thanks..

03-16-2011, 01:15 AM	#4
Jose Blanca Member Location: Valencia, Spain Join Date: Aug 2009 Posts: 70	We usually merge bam files for GATK. Our code is exposed in a pipeline (http://bioinf.comav.upv.es/ngs_backbone/), but if you like python you could use the underlying library (https://github.com/JoseBlanca/franklin). Regards.