Effective subsampling of BAMs
I was trying to subsample WES BAM files with samtools view -s on coverage 75. My samples had mean coverage in target regions 195 and 130 so I used fractions 100/195 =0.51 and 100/130=0.76, when I subsampled them with samtools and recalculated coverage it was around 65-68. What I did wrong? If you have any ideas of other tools how to effectively subsample BAMs on the same number of reads or on the same coverage, please let me know.
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ATpoint
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esimonova.me •
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I have some code here A: Subsampling Bam File With Samtools to use sambamba for the subsampling. You can specify a number of reads rather than a fraction, maybe that helps.
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