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Handling input of non-standard chromosomes (VCF) #159

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smlmbrt opened this issue Aug 24, 2023 · 0 comments · Fixed by #169 or #187
Closed

Handling input of non-standard chromosomes (VCF) #159

smlmbrt opened this issue Aug 24, 2023 · 0 comments · Fixed by #169 or #187
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enhancement New feature or request

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@smlmbrt
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smlmbrt commented Aug 24, 2023

Description of feature

Users commonly need to adjust the VCF import to --allow-extra-chr (see #35 #132 #143). We should correct the pipeline to not error out at this stage, and perhaps allow the extra chromosomes as input but only allow output of reference autosomes and sex-chromosomes using --chr 1-22, X, Y, XY or something similar.
@smlmbrt smlmbrt added the enhancement New feature or request label Aug 24, 2023
@smlmbrt smlmbrt changed the title Non-standard chromosomes Handling input of non-standard chromosomes Aug 24, 2023
@smlmbrt smlmbrt linked a pull request Sep 14, 2023 that will close this issue
Avoid plink2_vcf errors #169
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@smlmbrt smlmbrt changed the title Handling input of non-standard chromosomes Handling input of non-standard chromosomes (VCF) Sep 15, 2023
@smlmbrt smlmbrt linked a pull request Oct 3, 2023 that will close this issue
v2.0.0-alpha.3 #187
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Avoid plink2_vcf errors PGScatalog/pgsc_calc
v2.0.0-alpha.3 PGScatalog/pgsc_calc
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