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bam files header

maripezmaripez argentinaMember

Hi, I am new in gatk, and as bioinformatician too
I am trying to analyze some public bam files; it included all the genome but I am only interested in plastome genomes. I need to obtain variants from the plastome; so I first extracted Pt reads using samtools view (including the header). Then I tried to eliminate all the other chromosomes and scaffolds from the header to do haplotype caller using the Pt.fasta as reference; I extracted the headers, eliminated the unnecessary lines with sed and finally I did samtools reheader... but he files could not be indexed, "bus error". I don't exactly understand what I am doing wrong; the correcter headers look like the .dict file from the reference, Can you please help me?? Thanks!!

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