Post date: Jun 25, 2020 6:6:9 PM
(base) Rozenns-MacBook-Pro:ibd rozenn$ plink --vcf ../vcf/friends_4rd.vcf --recode --allow-extra-chr --out friend
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 friend.log.
Options in effect:
--allow-extra-chr
--out friend
--recode
--vcf ../vcf/friends_4rd.vcf
16384 MB RAM detected; reserving 8192 MB for main workspace.
--vcf: friend-temporary.bed + friend-temporary.bim + friend-temporary.fam
written.
39164 variants loaded from .bim file.
117 people (0 males, 0 females, 117 ambiguous) loaded from .fam.
Ambiguous sex IDs written to friend.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 117 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.962985.
39164 variants and 117 people pass filters and QC.
Note: No phenotypes present.
--recode ped to friend.ped + friend.map ... done.
(base) Rozenns-MacBook-Pro:ibd rozenn$ plink --file friend --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 friend
--genome
16384 MB RAM detected; reserving 8192 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (39164 variants, 117 people).
--file: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam
written.
39164 variants loaded from .bim file.
117 people (0 males, 0 females, 117 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
Using up to 4 threads (change this with --threads).
Before main variant filters, 117 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.962985.
39164 variants and 117 people pass filters and QC.
Note: No phenotypes present.
IBD calculations complete.
Finished writing plink.genome .