Post date: Jun 07, 2020 1:25:44 PM
This time I use the same technique of filtering based on AN number, but focusing on "friends only" vcf file.
size of original vcf - 198319 filtered2xHiCov_pando_friends_variants.vcf
filter for 300 AN - 168756 friends_AN_300.vcf --> 198319 - 168756 = 29563 out of 33499 total SNPs --> left with 3936 SNPs
Try IBD on this set.
Plink commands:
(base) Rozenns-MacBook-Pro:IBD_friends_AN_300 rozenn$ plink --vcf friends_AN_300.vcf --recode --allow-extra-chr --out f_AN_300
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 f_AN_300.log.
Options in effect:
--allow-extra-chr
--out f_AN_300
--recode
--vcf friends_AN_300.vcf
16384 MB RAM detected; reserving 8192 MB for main workspace.
--vcf: f_AN_300-temporary.bed + f_AN_300-temporary.bim + f_AN_300-temporary.fam
written.
3936 variants loaded from .bim file.
154 people (0 males, 0 females, 154 ambiguous) loaded from .fam.
Ambiguous sex IDs written to f_AN_300.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 154 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.978362.
3936 variants and 154 people pass filters and QC.
Note: No phenotypes present.
--recode ped to f_AN_300.ped + f_AN_300.map ... done.
(base) Rozenns-MacBook-Pro:IBD_friends_AN_300 rozenn$ plink --file f_AN_300 --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 f_AN_300
--genome
16384 MB RAM detected; reserving 8192 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (3936 variants, 154 people).
--file: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam
written.
3936 variants loaded from .bim file.
154 people (0 males, 0 females, 154 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
Using up to 4 threads (change this with --threads).
Before main variant filters, 154 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.978362.
3936 variants and 154 people pass filters and QC.
Note: No phenotypes present.
IBD calculations complete.
Finished writing plink.genome .
filter 2:
164933 ../../8-DefineClones/friends_AN_306.vcf --> 198319 - 164933 - 33499 = -113
(base) Rozenns-MacBook-Pro:IBD_friends_AN_306 rozenn$ plink --vcf friends_AN_306.vcf --recode --allow-extra-chr --out f_AN_306
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 f_AN_306.log.
Options in effect:
--allow-extra-chr
--out f_AN_306
--recode
--vcf friends_AN_306.vcf
16384 MB RAM detected; reserving 8192 MB for main workspace.
--vcf: f_AN_306-temporary.bed + f_AN_306-temporary.bim + f_AN_306-temporary.fam
written.
113 variants loaded from .bim file.
154 people (0 males, 0 females, 154 ambiguous) loaded from .fam.
Ambiguous sex IDs written to f_AN_306.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 154 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.993736.
113 variants and 154 people pass filters and QC.
Note: No phenotypes present.
--recode ped to f_AN_306.ped + f_AN_306.map ... done.
(base) Rozenns-MacBook-Pro:IBD_friends_AN_306 rozenn$ plink --file f_AN_306 --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 f_AN_306
--genome
16384 MB RAM detected; reserving 8192 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (113 variants, 154 people).
--file: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam
written.
113 variants loaded from .bim file.
154 people (0 males, 0 females, 154 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
Using up to 4 threads (change this with --threads).
Before main variant filters, 154 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.993736.
113 variants and 154 people pass filters and QC.
Note: No phenotypes present.
IBD calculations complete.
Finished writing plink.genome .