Variant calling from merged bam file with one vcf output
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6 weeks ago
askif4 ▴ 10

I have merged two different bam files with same @RG ids (with picard)

When I looked into the bam file however,

enter image description here

I found that the name "test" has changed.

I have matched the IDs for variant calling for one merged bam file.

When I tried merging different bam files and did normal variant calling, the output vcf file had more than one sample columns at the end. (the image below is an example for sample columns)

enter image description here

I want that sample column to be one.

How can I make merged bam files to be considered as one big bam file?

bam WGS variant calling • 101 views

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