Variant formatter uses GRCh37 instead of GRCh37.p13

molgenis / data-transform-vkgl

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Variant formatter uses GRCh37 instead of GRCh37.p13 #25

Open dennishendriksen opened 4 years ago

dennishendriksen commented 4 years ago

https://github.com/molgenis/data-transform-vkgl/blob/e14e871174413031d9044d8b11bc6884fedd64dd/docker/variant-formatter/server.py#L20

GRCh37 is the original unpatched GRCh37 (GCA_000001405.1) and differs from GRCh37.p13 (GCA_000001405.14) which is reference sequence used by Alissa Interpret.

dennishendriksen commented 3 years ago

Candidates:

hg19 (ucsc.hg19.fasta)
b37 (Homo_sapiens_assembly19.fasta)
GRCh37 (GRCh37.p13.genome.fasta)
humanG1Kv37 (human_g1k_v37.fasta)
humanG1Kv37_phiX (human_g1k_v37_phiX.fasta)

context: https://gatk.broadinstitute.org/hc/en-us/articles/360035890711-GRCh37-hg19-b37-humanG1Kv37-Human-Reference-Discrepancies#comparison