Hello, I wanted to extract the allele counts and homozygotes count from gnomad v211 and v31. I followed the command from this thread and I was able to get the output in form of TSV, however I want the output in vcf format. Trying to export the same as VCF gives me only loci and ref/alt. The comma…

Hail exports the fields of struct info as INFO fields, the elements of set<str> filters as FILTERS, the value of str rsid as ID, and the value of float64 qual as QUAL. No other row fields are exported. – https://hail.is/docs/0.2/methods/impex.html#hail.methods.export_vcf The table being exported…

Hay @nawatts the command worked well, I was able to extract the file that I wanted! I could not figure out how to load data as struct, this command does it easily. I think I should spend more time in Python :sweat:

Hello, I was able to extract the vcf for Gnomad v211 data, but I’m running out of memory when I’m trying to extract the same data from Gnomad v3.1 data. Here is the last line of error. I can post the full error if it’s required - Hail version: 0.2.61-3c86d3ba497a Error summary: OutOfMemoryError: G…

I set memory to 180G, still got this error - Stage 0:> (0 + 56) / 115376] Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "refresh progress" Traceback (most recent call last): File "<stdin>", line 1, in <m…

No, this is a different issue. What is your full pipeline?

Hay, turns out I hadn’t copied the PYSPARK_ARGUMENTS correctly. It worked when I coped the entire line and used my appropriate amount of memory. Thanks!

Extracting gnomad counts into a vcf file

Hail Query & hailctl

tpoterba March 8, 2021, 1:22pm 5

See here for how to set memory configurations using the PYSPARK_SUBMIT_ARGS environment var: Java Heap Space out of memory - #5 by yl3336

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Extracting gnomad counts into a vcf file

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