"convert_gtex_to_rsids" does not work for InDels.

MCorentin / vargen

VarGen is an R package designed to get a list of variants related to a disease. It just need an OMIM morbid ID as input and optionally a list of tissues / gwas traits of interest to complete the results. You can also use your own customised list of genes. VarGen is capable of annotating the variants to help you identify the most impactful ones.

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"convert_gtex_to_rsids" does not work for InDels. #1

Closed MCorentin closed 4 years ago

MCorentin commented 4 years ago

GTEx and Ensembl do not use the same position to refer to the same InDels.

For example with 1_760811_CTCTT_C_b37 (rs200712425).

GTEx format: CTCTT becomes C.
Ensembl format: TCTTTCTTT becomes TCTTT.

In both cases "TCTT" gets deleted, but GTEx refers it from the left (position 760811) and ensembl from the right (position 760812).

Since VarGen uses the position to translate the GTEx id to rsid, "convert_gtex_to_rsids" does not work for InDels.

MCorentin commented 4 years ago

Solved with commit 2ed3488d5976275104647eeae2c87a5f759a0c1