Bins for dp_hist_all_bin_freq

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James Melhorn

• July 23, 2024 19:51

Please could somebody explain what the bins are for this output histogram. I am presuming this refers to allelic depth. 

dp_hist_all_bin_freq

Unfortunately, I can't seem to find an explanation.

Many thanks,

James

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  Gökalp Çelik

  • July 24, 2024 08:03

  Hi James Melhorn

  I am not 100% sure about it however it looks like those values are used to display site metrics within gnomAD browser like below. I will ask our variant team and try to come up with a better explanation. 

  

  Regards. 

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  Gökalp Çelik

  • July 24, 2024 13:36

  Hi again. 

  I was right about it. Here is a brief showing of how that data is used. 

  This is a sample site 

  Y    21885356    rs1282732903    T    C    159.48    AC0    dp_hist_all_bin_freq=103697|12874|6732|1946|419|63|11|4|1|0|1|0|0|0|0|0|0|0|0|0

  for brevity I removed all other INFO fields. 

  These numbers match to those bins described in the gnomAD v2.1 header section.

  ##INFO=<ID=dp_hist_alt_bin_freq,Number=A,Type=String,Description="Histogram for DP in heterozygous individuals; bin edges are: 0|5|10|15|20|25|30|35|40|45|50|55|60|65|70|75|80|85|90|95|100">
  ##INFO=<ID=dp_hist_alt_n_larger,Number=A,Type=Integer,Description="Count of DP values falling above highest histogram bin edge">
  ##INFO=<ID=dp_hist_all_bin_freq,Number=A,Type=String,Description="Histogram for DP; bin edges are: 0|5|10|15|20|25|30|35|40|45|50|55|60|65|70|75|80|85|90|95|100">
  ##INFO=<ID=dp_hist_all_n_larger,Number=A,Type=Integer,Description="Count of DP values falling above highest histogram bin edge">

  And here is the visual depiction of those numbers.

  

  When you hover over all the bins in the histogram you should be able to see those numbers that are encoded in the INFO field.

  More information can be obtained from the gnomAD browser page and there is even a support email that you can use to ask further questions to our gnomAD team. 

  I hope this helps. 

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