Missing read depth mean after filter_entries() #3742
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iris-garden
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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.
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!
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