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francois-a / fastqtl

Enhanced version of the FastQTL QTL mapper
GNU General Public License v3.0
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multi-alleles VCF #5

Closed lyd0527 closed 5 years ago

lyd0527 commented 6 years ago

Hi,

Does FastQTL support multi-alleles VCF for input file such as CNV? Besides, How do I caculate the DS value? Thank you~

Best,

Yuanda

francois-a commented 6 years ago

Multi-allelic sites need to be split into pairs of biallelic representations. DS is calculated automatically from the GT field if that is present.

lyd0527 commented 6 years ago

If we split the multi-alleles to the biallelic pair, each pair will have many missing value. Do you know if some software such as matrix_eQTL support multi-alleles input ? Thank you.

francois-a commented 6 years ago

I'm not aware of existing QTL mappers that handle multi-allelic sites. FastQTL will impute the missing samples for these sites to the mean.