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Who made the VCF file? samtools also will downsample during genotype calling. In this case, I see it reports allele depths of 4 and 2, and…
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Thank you for answering, and I have tried to follow your instruction to turn the downsampling off in preference, but they are still d…
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Guess you forgot to attach the image. You can edit the post above and add that.
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Files included in this link are technical replicates from lanes 1 through 4 and have the same `S21` number: https://www.encodeproject.org/e…
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See the answer here as an option -->https://www.biostars.org/p/446822/
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