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molgenis / systemsgenetics

Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool
https://github.com/molgenis/systemsgenetics/wiki
GNU General Public License v3.0
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how to extract the expression numerical matrix of SNPS? #672

Closed ChaoXianSen closed 3 months ago

ChaoXianSen commented 3 months ago

java -jar GenotypeHarmonizer.jar \ -i ./all.sample.raw.snp.vcf.gz \ -I VCF \ -O TRITYPER \ -o GenotypeHarmonizer \ -mf 0.05 -ip 0.4 -asf

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Are there any tools or methods for extracting the expression numerical matrix of SNPS ? Expression value matrix was extracted for subsequent mediation analysis. Looking forward to reply, thank you!

PatrickDeelen commented 3 months ago

You can try -O TABLE to get the dosages.

ChaoXianSen commented 3 months ago

Thank you for your reply! image image

What are the rules of mutation site conversion, how is it converted to numerical values ？

Looking forward to reply again, thank you!

PatrickDeelen commented 3 months ago

These are genotype dosages in the sense they are also used by other formats, ie the count of the alternative allele and -1 for missing.