Hi all,
I have two bam files, bam1 and bam2 with two different read groups. I would like GATK to treat as a single sample and do the SNP calling. And it can be done by giving same read group names to both the bam files and call SNP's by pooling them to a single bam file.
But my interest is, Lets say a SNP i covered by 30 reads, i am interested in finding out number of reads that have come from bam1 and number of reads from bam2.
How can we distinguish between the reads from two bam files after merging them into a single bam file with same read group name?
Is there a way or any tool to achieve this? Any suggestions!!!
I have two bam files, bam1 and bam2 with two different read groups. I would like GATK to treat as a single sample and do the SNP calling. And it can be done by giving same read group names to both the bam files and call SNP's by pooling them to a single bam file.
But my interest is, Lets say a SNP i covered by 30 reads, i am interested in finding out number of reads that have come from bam1 and number of reads from bam2.
How can we distinguish between the reads from two bam files after merging them into a single bam file with same read group name?
Is there a way or any tool to achieve this? Any suggestions!!!
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