Post date: Jun 04, 2020 10:12:33 PM
# when filtered against both friends and PON
(base) Rozenns-MacBook-Pro:ibd_pando_80 rozenn$ plink --vcf pando_minus_all_SNPs_80_with_header.vcf --recode --allow-extra-chr --out pando_all_80
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_all_80.log.
Options in effect:
--allow-extra-chr
--out pando_all_80
--recode
--vcf pando_minus_all_SNPs_80_with_header.vcf
16384 MB RAM detected; reserving 8192 MB for main workspace.
--vcf: pando_all_80-temporary.bed + pando_all_80-temporary.bim +
pando_all_80-temporary.fam written.
8826 variants loaded from .bim file.
109 people (0 males, 0 females, 109 ambiguous) loaded from .fam.
Ambiguous sex IDs written to pando_all_80.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 0.943581.
8826 variants and 109 people pass filters and QC.
Note: No phenotypes present.
--recode ped to pando_all_80.ped + pando_all_80.map ... done.
(base) Rozenns-MacBook-Pro:ibd_pando_80 rozenn$ plink --file pando_all_80 --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_all_80
--genome
16384 MB RAM detected; reserving 8192 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (8826 variants, 109 people).
--file: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam
written.
8826 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 0.943581.
8826 variants and 109 people pass filters and QC.
Note: No phenotypes present.
IBD calculations complete.
Finished writing plink.genome .
# when filtered against friends only
(base) Rozenns-MacBook-Pro:ibd_pando_80 rozenn$ plink --vcf pando_minus_friends_SNPs_80_with_header.vcf --recode --allow-extra-chr --out pando_friends_80
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_friends_80.log.
Options in effect:
--allow-extra-chr
--out pando_friends_80
--recode
--vcf pando_minus_friends_SNPs_80_with_header.vcf
16384 MB RAM detected; reserving 8192 MB for main workspace.
--vcf: pando_friends_80-temporary.bed + pando_friends_80-temporary.bim +
pando_friends_80-temporary.fam written.
9981 variants loaded from .bim file.
109 people (0 males, 0 females, 109 ambiguous) loaded from .fam.
Ambiguous sex IDs written to pando_friends_80.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 0.94674.
9981 variants and 109 people pass filters and QC.
Note: No phenotypes present.
--recode ped to pando_friends_80.ped + pando_friends_80.map ... done.
(base) Rozenns-MacBook-Pro:ibd_pando_80 rozenn$ plink --file pando_friends_80 --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_friends_80
--genome
16384 MB RAM detected; reserving 8192 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (9981 variants, 109 people).
--file: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam
written.
9981 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 0.94674.
9981 variants and 109 people pass filters and QC.
Note: No phenotypes present.
IBD calculations complete.
Finished writing plink.genome .