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TonyKess / seaage_GWAS Public

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seaage_GWAS

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11.ANGSD_GWAS

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12 lines (10 loc) · 347 Bytes

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seaage_GWAS

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11.ANGSD_GWAS

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12 lines (10 loc) · 347 Bytes

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cd /home/tkess/scratch/Salmon_AOM/seaage/CIGENE_align

/home/tkess/angsd/angsd \

-doMaf 4 \

-vcf-gp Salmo_ssa01_CIGENE_80geno_hd.vcf.gz \

-fai /home/tkess/scratch/Salmon_CIGENE_Ref/reference/CIGENE-ICSASG_v2.fa.fai \

-yBin All_Ageclass_HD.txt \

-out GWAS_out/All_hd_ssa01_2PC \

-doAsso 4 \

-cov All_HD_PCA_12.txt \

-nthreads 10

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