hi, as I am still learning hail (python), I have a very basic question, because I do not yet fully understand hail tables and how to query them. I want to get allele frequencies for all gnomAD populations for a subset of variants and export it as table or vcf. I tried exemplarily for one random va…

Sorry, my earlier example incorrectly included the locus and alleles key fields in the select. It should have been: ht.select( gnomad_ac=ht.freq[0].AC, gnomad_af=ht.freq[0].AF, gnomad_an=ht.freq[0].AN, gnomad_homozygote_count=ht.freq[0].homozygote_count, ).export("/path/to/export.tsv")

The gnomAD Hail Tables have a global field named freq_meta. Each entry in freq_meta describes the freq entry at the same index (freq_meta[0] contains information about freq[0], freq_meta[1] about freq[1], etc.). To get freq_meta as a Python list, use hl.eval(ht.globals.freq_meta).

Thanks! That already helps. Again, sorry for the basic questions, but can you tell me how to combine this information to: a) generate a ht with e.g. freq[0] and freq[2] and b) finally export it to a tab, tsv or csv delimited text file which looks like this: locus | alleles | gnomAD.AC | gnomAD…

Something along the lines of: ht.select( "locus", "alleles", gnomad_ac=ht.freq[0].AC, gnomad_af=ht.freq[0].AF, gnomad_an=ht.freq[0].AN, gnomad_homozygote_count=ht.freq[0].homozygote_count, ).export("/path/to/export.tsv") To include more columns, include expressions for them in the sele…

Thanks a lot, that really helped. It worked without the “locus”, “alleles” part.

Hello, I want to extract the counts but for the whole genome, not just few lociis. I downloaded gnomad v211 liftover ht and ran the command, I met the following error - 2021-03-02 17:09:23 Hail: ERROR: Analysis exception: 'Table.select': cannot overwrite key field 'locus' with annotate, select or …

Hello @nawatts and @tpoterba , I tried this command ht.select( gnomad_ac=ht.freq[0].AC, gnomad_af=ht.freq[0].AF, gnomad_an=ht.freq[0].AN, gnomad_homozygote_count=ht.freq[0].homozygote_count, ).export("gnomad_v211_genome_counts.tsv") and it worked without issue, but the locus and all…

That would look something like: ht.select( chr=ht.locus.contig, tStart=ht.locus.position, tRef=ht.alleles[0], tAlt=ht.alleles[1], tAC=ht.freq[0].AC, Homozygotes=ht.freq[0].homozygote_count, ).export("file.tsv") I’m not sure what tEnd would refer to. The gnomAD variants have a single lo…

@kvn95ss , If your table uses the locus and alleles and key fields (check ht.describe()), you’ll need to. run ht = ht.key_by() first.

Gnomad allele frequency query

Hail Query & hailctl

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Gnomad allele frequency query

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