BAM to FASTA with uncovered regions
Dear All! I work on archaic DNA (mitochondrial in this case), and due to the aDNA's nature, the final assembly has gaps in it. I have BAM files and I want to convert them to FASTA, so I used samtools fasta command for it, but then I got multiple FASTA's per a single BAM, one FASTA one for one covered region in the same mtGenome. But I want to make a single FASTA file for each BAM, where the uncovered regions are present with Ns. Also I want to adjust the sequencing depth. Can anyone help me? Thanks in advance :)
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gerberd1990 •
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