Post date: May 26, 2020 2:38:14 PM
IBD in Pando
(base) Rozenns-MacBook-Pro:1-find_proba_hets rozenn$ plink --vcf filtered2xHiCov_pando_only_variants.vcf --recode --allow-extra-chr --out pando
PLINK v1.90b6.17 64-bit (28 Apr 2020) www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to pando.log.
Options in effect:
--allow-extra-chr
--out pando
--recodeß
--vcf filtered2xHiCov_pando_only_variants.vcf
16384 MB RAM detected; reserving 8192 MB for main workspace.
--vcf: pando-temporary.bed + pando-temporary.bim + pando-temporary.fam written.
15543 variants loaded from .bim file.
109 people (0 males, 0 females, 109 ambiguous) loaded from .fam.
Ambiguous sex IDs written to pando.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 109 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.952238.
15543 variants and 109 people pass filters and QC.
Note: No phenotypes present.
--recode ped to pando.ped + pando.map ... done.
(base) Rozenns-MacBook-Pro:1-find_proba_hets rozenn$ plink --file pando --genome --allow-extra-chr
PLINK v1.90b6.17 64-bit (28 Apr 2020) www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to plink.log.
Options in effect:
--allow-extra-chr
--file pando
--genome
16384 MB RAM detected; reserving 8192 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (15543 variants, 109 people).
--file: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam
written.
15543 variants loaded from .bim file.
109 people (0 males, 0 females, 109 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
Using up to 4 threads (change this with --threads).
Before main variant filters, 109 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.952238.
15543 variants and 109 people pass filters and QC.
Note: No phenotypes present.
IBD calculations complete.
Finished writing plink.genome