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NEFSC · Nov 5, 2024 · 8313750 · 8313750
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diff --git a/.../Popgen/angsd/F0_Broodstock/parentage.csv → ...t/Popgen/angsd/F0Broodstock_parentage.csv b/.../Popgen/angsd/F0_Broodstock/parentage.csv → ...t/Popgen/angsd/F0Broodstock_parentage.csv
diff --git a/....05_majorminor4_minind25_minD5x125_maxD20x500minDind5_maxDind150_minq30_minmapQ.beagle.gz b/....05_majorminor4_minind25_minD5x125_maxD20x500minDind5_maxDind150_minq30_minmapQ.beagle.gz
diff --git a/....05_majorminor4_minind25_minD5x125_maxD20x500minDind5_maxDind150_minq30_minmapQ.counts.gz b/....05_majorminor4_minind25_minD5x125_maxD20x500minDind5_maxDind150_minq30_minmapQ.counts.gz
diff --git a/...f0.05_majorminor4_minind25_minD5x125_maxD20x500minDind5_maxDind150_minq30_minmapQ.geno.gz b/...f0.05_majorminor4_minind25_minD5x125_maxD20x500minDind5_maxDind150_minq30_minmapQ.geno.gz
diff --git a/...af0.05_majorminor4_minind25_minD5x125_maxD20x500minDind5_maxDind150_minq30_minmapQ.ibs.gz b/...af0.05_majorminor4_minind25_minD5x125_maxD20x500minDind5_maxDind150_minq30_minmapQ.ibs.gz
diff --git a/...f0.05_majorminor4_minind25_minD5x125_maxD20x500minDind5_maxDind150_minq30_minmapQ.mafs.gz b/...f0.05_majorminor4_minind25_minD5x125_maxD20x500minDind5_maxDind150_minq30_minmapQ.mafs.gz
diff --git a/...af0.05_majorminor4_minind25_minD5x125_maxD20x500minDind5_maxDind150_minq30_minmapQ.pos.gz b/...af0.05_majorminor4_minind25_minD5x125_maxD20x500minDind5_maxDind150_minq30_minmapQ.pos.gz
diff --git a/HPC_analysis/output/Popgen/angsd/F0_Broodstock/ID b/HPC_analysis/output/Popgen/angsd/F0_Broodstock/ID
diff --git a/...af0.05_majorminor4_minind321_minD5x1605_maxD20x6420minDind5_maxDind150_minq30_minmapQ.bcf b/...af0.05_majorminor4_minind321_minD5x1605_maxD20x6420minDind5_maxDind150_minq30_minmapQ.bcf
diff --git a/..._majorminor4_minind321_minD5x1605_maxD20x6420minDind5_maxDind150_minq30_minmapQ.beagle.gz b/..._majorminor4_minind321_minD5x1605_maxD20x6420minDind5_maxDind150_minq30_minmapQ.beagle.gz
diff --git a/...05_majorminor4_minind321_minD5x1605_maxD20x6420minDind5_maxDind150_minq30_minmapQ.geno.gz b/...05_majorminor4_minind321_minD5x1605_maxD20x6420minDind5_maxDind150_minq30_minmapQ.geno.gz
diff --git a/...05_majorminor4_minind321_minD5x1605_maxD20x6420minDind5_maxDind150_minq30_minmapQ.mafs.gz b/...05_majorminor4_minind321_minD5x1605_maxD20x6420minDind5_maxDind150_minq30_minmapQ.mafs.gz
diff --git a/...majorminor4_minind321_minD5x1605_maxD20x6420minDind5_maxDind150_minq30_minmapQ.vcf.gz.csi b/...majorminor4_minind321_minD5x1605_maxD20x6420minDind5_maxDind150_minq30_minmapQ.vcf.gz.csi
diff --git a/HPC_analysis/output/Popgen/angsd/F0_Broodstock_all_juveniles/F0_OM_plink.bed b/HPC_analysis/output/Popgen/angsd/F0_Broodstock_all_juveniles/F0_OM_plink.bed
diff --git a/HPC_analysis/output/Popgen/angsd/F0_Broodstock_all_juveniles/F0_OM_plink.log b/HPC_analysis/output/Popgen/angsd/F0_Broodstock_all_juveniles/F0_OM_plink.log
diff --git a/...af0.05_majorminor4_minind321_minD5x1605_maxD20x6420minDind5_maxDind150_minq30_minmapQ.bcf b/...af0.05_majorminor4_minind321_minD5x1605_maxD20x6420minDind5_maxDind150_minq30_minmapQ.bcf
diff --git a/...0.05_majorminor4_minind19_minD5x95_maxD20x380minDind5_maxDind150_minq30_minmapQ.beagle.gz b/...0.05_majorminor4_minind19_minD5x95_maxD20x380minDind5_maxDind150_minq30_minmapQ.beagle.gz
diff --git a/...0.05_majorminor4_minind19_minD5x95_maxD20x380minDind5_maxDind150_minq30_minmapQ.counts.gz b/...0.05_majorminor4_minind19_minD5x95_maxD20x380minDind5_maxDind150_minq30_minmapQ.counts.gz
diff --git a/...af0.05_majorminor4_minind19_minD5x95_maxD20x380minDind5_maxDind150_minq30_minmapQ.geno.gz b/...af0.05_majorminor4_minind19_minD5x95_maxD20x380minDind5_maxDind150_minq30_minmapQ.geno.gz
diff --git a/...Maf0.05_majorminor4_minind19_minD5x95_maxD20x380minDind5_maxDind150_minq30_minmapQ.ibs.gz b/...Maf0.05_majorminor4_minind19_minD5x95_maxD20x380minDind5_maxDind150_minq30_minmapQ.ibs.gz
diff --git a/...af0.05_majorminor4_minind19_minD5x95_maxD20x380minDind5_maxDind150_minq30_minmapQ.mafs.gz b/...af0.05_majorminor4_minind19_minD5x95_maxD20x380minDind5_maxDind150_minq30_minmapQ.mafs.gz
diff --git a/...Maf0.05_majorminor4_minind19_minD5x95_maxD20x380minDind5_maxDind150_minq30_minmapQ.pos.gz b/...Maf0.05_majorminor4_minind19_minD5x95_maxD20x380minDind5_maxDind150_minq30_minmapQ.pos.gz
diff --git a/...analysis/output/Popgen/angsd/F1_Broodstock/F1_Broodstock_75/F1Broodstock_pH75_norm.vcf.gz b/...analysis/output/Popgen/angsd/F1_Broodstock/F1_Broodstock_75/F1Broodstock_pH75_norm.vcf.gz
diff --git a/HPC_analysis/output/Popgen/angsd/F1_Broodstock/F1_Broodstock_75/IDs.txt b/HPC_analysis/output/Popgen/angsd/F1_Broodstock/F1_Broodstock_75/IDs.txt
diff --git a/....05_majorminor4_minind20_minD5x100_maxD20x400minDind5_maxDind150_minq30_minmapQ.beagle.gz b/....05_majorminor4_minind20_minD5x100_maxD20x400minDind5_maxDind150_minq30_minmapQ.beagle.gz
diff --git a/....05_majorminor4_minind20_minD5x100_maxD20x400minDind5_maxDind150_minq30_minmapQ.counts.gz b/....05_majorminor4_minind20_minD5x100_maxD20x400minDind5_maxDind150_minq30_minmapQ.counts.gz
diff --git a/...f0.05_majorminor4_minind20_minD5x100_maxD20x400minDind5_maxDind150_minq30_minmapQ.geno.gz b/...f0.05_majorminor4_minind20_minD5x100_maxD20x400minDind5_maxDind150_minq30_minmapQ.geno.gz
diff --git a/...af0.05_majorminor4_minind20_minD5x100_maxD20x400minDind5_maxDind150_minq30_minmapQ.ibs.gz b/...af0.05_majorminor4_minind20_minD5x100_maxD20x400minDind5_maxDind150_minq30_minmapQ.ibs.gz
diff --git a/...f0.05_majorminor4_minind20_minD5x100_maxD20x400minDind5_maxDind150_minq30_minmapQ.mafs.gz b/...f0.05_majorminor4_minind20_minD5x100_maxD20x400minDind5_maxDind150_minq30_minmapQ.mafs.gz
diff --git a/...af0.05_majorminor4_minind20_minD5x100_maxD20x400minDind5_maxDind150_minq30_minmapQ.pos.gz b/...af0.05_majorminor4_minind20_minD5x100_maxD20x400minDind5_maxDind150_minq30_minmapQ.pos.gz
diff --git a/HPC_analysis/output/Popgen/angsd/F1_Broodstock/F1_Broodstock_8/F1Broodstock_pH8_norm.vcf.gz b/HPC_analysis/output/Popgen/angsd/F1_Broodstock/F1_Broodstock_8/F1Broodstock_pH8_norm.vcf.gz
diff --git a/HPC_analysis/output/Popgen/angsd/F1_Broodstock/F1_Broodstock_8/IDs.txt b/HPC_analysis/output/Popgen/angsd/F1_Broodstock/F1_Broodstock_8/IDs.txt
diff --git a/HPC_analysis/output/Popgen/angsd/F1_Broodstock/F1_Broodstock_output.bed b/HPC_analysis/output/Popgen/angsd/F1_Broodstock/F1_Broodstock_output.bed
diff --git a/HPC_analysis/output/Popgen/angsd/F1_Broodstock/F1_Broodstock_output.fam b/HPC_analysis/output/Popgen/angsd/F1_Broodstock/F1_Broodstock_output.fam
diff --git a/HPC_analysis/output/Popgen/angsd/F1_Broodstock/PCA/F1_Broodstock_PC1.pdf b/HPC_analysis/output/Popgen/angsd/F1_Broodstock/PCA/F1_Broodstock_PC1.pdf
diff --git a/HPC_analysis/output/Popgen/angsd/F1_Broodstock/PCA/F1_Broodstock_PCA_initial.pdf b/HPC_analysis/output/Popgen/angsd/F1_Broodstock/PCA/F1_Broodstock_PCA_initial.pdf
diff --git a/HPC_analysis/output/Popgen/angsd/F1_Broodstock/PCA/F1_Screeplot.pdf b/HPC_analysis/output/Popgen/angsd/F1_Broodstock/PCA/F1_Screeplot.pdf
diff --git a/...nalysis/output/Popgen/angsd/F1_Broodstock/heterozygosity/F1_Broodstock_heterozygosity.txt b/...nalysis/output/Popgen/angsd/F1_Broodstock/heterozygosity/F1_Broodstock_heterozygosity.txt
diff --git a/...sis/output/Popgen/angsd/F1_Broodstock/heterozygosity/F1_Broodstock_obs_heterozygosity.pdf b/...sis/output/Popgen/angsd/F1_Broodstock/heterozygosity/F1_Broodstock_obs_heterozygosity.pdf
diff --git a/....05_majorminor4_minind38_minD5x190_maxD20x760minDind5_maxDind150_minq30_minmapQ.beagle.gz b/....05_majorminor4_minind38_minD5x190_maxD20x760minDind5_maxDind150_minq30_minmapQ.beagle.gz
diff --git a/....05_majorminor4_minind38_minD5x190_maxD20x760minDind5_maxDind150_minq30_minmapQ.counts.gz b/....05_majorminor4_minind38_minD5x190_maxD20x760minDind5_maxDind150_minq30_minmapQ.counts.gz
diff --git a/...f0.05_majorminor4_minind38_minD5x190_maxD20x760minDind5_maxDind150_minq30_minmapQ.geno.gz b/...f0.05_majorminor4_minind38_minD5x190_maxD20x760minDind5_maxDind150_minq30_minmapQ.geno.gz
diff --git a/...af0.05_majorminor4_minind38_minD5x190_maxD20x760minDind5_maxDind150_minq30_minmapQ.ibs.gz b/...af0.05_majorminor4_minind38_minD5x190_maxD20x760minDind5_maxDind150_minq30_minmapQ.ibs.gz
diff --git a/...f0.05_majorminor4_minind38_minD5x190_maxD20x760minDind5_maxDind150_minq30_minmapQ.mafs.gz b/...f0.05_majorminor4_minind38_minD5x190_maxD20x760minDind5_maxDind150_minq30_minmapQ.mafs.gz
diff --git a/...af0.05_majorminor4_minind38_minD5x190_maxD20x760minDind5_maxDind150_minq30_minmapQ.pos.gz b/...af0.05_majorminor4_minind38_minD5x190_maxD20x760minDind5_maxDind150_minq30_minmapQ.pos.gz
diff --git a/HPC_analysis/output/Popgen/angsd/F1_Juveniles/F1_Juveniles_75/F1Juveniles_pH75_norm.vcf.gz b/HPC_analysis/output/Popgen/angsd/F1_Juveniles/F1_Juveniles_75/F1Juveniles_pH75_norm.vcf.gz
diff --git a/HPC_analysis/output/Popgen/angsd/F1_Juveniles/F1_Juveniles_75/IDs.txt b/HPC_analysis/output/Popgen/angsd/F1_Juveniles/F1_Juveniles_75/IDs.txt
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diff --git a/...af0.05_majorminor4_minind35_minD5x175_maxD20x700minDind5_maxDind150_minq30_minmapQ.pos.gz b/...af0.05_majorminor4_minind35_minD5x175_maxD20x700minDind5_maxDind150_minq30_minmapQ.pos.gz
diff --git a/HPC_analysis/output/Popgen/angsd/F1_Juveniles/F1_Juveniles_8/F1Juveniles_pH8_norm.vcf.gz b/HPC_analysis/output/Popgen/angsd/F1_Juveniles/F1_Juveniles_8/F1Juveniles_pH8_norm.vcf.gz
diff --git a/HPC_analysis/output/Popgen/angsd/F1_Juveniles/F1_Juveniles_8/IDs.txt b/HPC_analysis/output/Popgen/angsd/F1_Juveniles/F1_Juveniles_8/IDs.txt
diff --git a/HPC_analysis/output/Popgen/angsd/F1_Juveniles/F1_Juveniles_Merged.bed b/HPC_analysis/output/Popgen/angsd/F1_Juveniles/F1_Juveniles_Merged.bed