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The following post was exported from discuss.hail.is, a forum for asking questions about Hail which has since been deprecated.
(Dec 18, 2023 at 14:38) barioux said:
Hi all,
Just wondered if you had a way to calculate the distribution of the mean read depth across all loci. I get ‘nan’ for dp_stats.mean at mean and std dev as follows after applying filter_entries.
This means that dp_stats.mean is NaN for at least one variant. You can use hl.is_nan with filter_rows to filter to a variant with a NaN for its dp_stats.mean.
dp_stats.mean is defined as hl.agg.stats(mt.DP). hl.agg.stats(...).mean is usually NaN when every entry is filtered or has a missing DP field. compute_entry_filter_stats can provide insight into which rows contain only filtered entries.
In particular, you probably have a SNP or INDEL where none of the entries have the minimum coverage.
The text was updated successfully, but these errors were encountered:
Note
The following post was exported from discuss.hail.is, a forum for asking questions about Hail which has since been deprecated.
(Dec 18, 2023 at 14:38) barioux said:
Hi all,
Just wondered if you had a way to calculate the distribution of the mean read depth across all loci. I get ‘nan’ for dp_stats.mean at mean and std dev as follows after applying filter_entries.
mt_filtered = mt.filter_entries(
((hl.is_snp(mt.alleles[0], mt.alleles[1]) & (mt.DP >= snv_min_coverage)) |
(hl.is_indel(mt.alleles[0], mt.alleles[1]) & (mt.DP >= indel_min_coverage)))
)
mt_filtered.variant_qc.dp_stats.summarize()
dp_stats.mean (float64 ):
Thanks in advance!
(Dec 18, 2023 at 19:29) danking said:
Hi barioux !
This means that
dp_stats.mean
isNaN
for at least one variant. You can usehl.is_nan
withfilter_rows
to filter to a variant with a NaN for its dp_stats.mean.dp_stats.mean
is defined ashl.agg.stats(mt.DP)
.hl.agg.stats(...).mean
is usually NaN when every entry is filtered or has a missingDP
field.compute_entry_filter_stats
can provide insight into which rows contain only filtered entries.In particular, you probably have a SNP or INDEL where none of the entries have the minimum coverage.
The text was updated successfully, but these errors were encountered: