bam > base_depth. . . Describe the solution you would like.

Samtools depth coverage

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You want "percentage coverage" rather than "coverage", which actually means "fold-coverage" (i.

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cov The output is pretty similar to samtools mpileup -f ref bam, ~1000x.

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ck. For example to get all the regions and count secondary, qc-fail and duplicated mappings/read: samtools-1.

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cram [in2. . . The scaling factor used is the inverse of the sequencing depth computed for the sample to match the 1x coverage. g. Passing zero for this option sets it to the highest possible value, effectively removing the depth limit.

samtools coverage -r chr1:1M-12M input.

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bam|in2.

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Where samtools depth outputs the position and depth for each base, it increments the number of covered positions in the respective bin.

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sam|in2.

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