BAM files just say "sample_ID"
None of my BAM files have a correct sample ID in their header, they all literally say "sample_ID"
I didn't catch this until after SNP calling. How can I get the BAM headers to have the name of the sample that they are? I have over 2,000 BAM files.
bam
snp
samtools
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Yikes ...............
Did the original file names have this information? You could perhaps
samtools reheaderthe files in that case.See as inspiration:
Bam Header Edit
Bam header editing
Some script including GNU parallel will probably help.