Post date: May 22, 2020 9:19:17 PM
Difference between SNP and SNV:
SNP has to appear in at least 1% of the population, may mean something about importance of this mutation, heredity.
SNV is used to talk about one variation, with no expectation about the frequency.
Useful info:
https://zzz.bwh.harvard.edu/plink/ibdibs.shtml#genome
Genetic mapping: which chromosome has each gene
Linkage mapping: map the genes that are on the same chromosome, contains the information about recombination frequency! (At each meiosis, mixing of chromosomes arms -- > mixing of alleles = recombination) frequency of re association tells about how far apart are the genes (two very close genes will migrate together most of the time. Two very far genes may end up on different arms)
(here we have a scattered genome, and no chromosomes defined - can this work?)
Use PLINK to calculate IBD in friends with the aim of distinguishing clones:
In terminal:
Rozenns-MacBook-Pro:5-friends rozenn$ plink --vcf filtered2xHiCov_pando_friends_variants.vcf --recode --allow-extra-chr --out friends
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 friends.log.
Options in effect:
--allow-extra-chr
--out friends
--recode
--vcf filtered2xHiCov_pando_friends_variants.vcf
16384 MB RAM detected; reserving 8192 MB for main workspace.
--vcf: friends-temporary.bed + friends-temporary.bim + friends-temporary.fam
written.
33499 variants loaded from .bim file.
154 people (0 males, 0 females, 154 ambiguous) loaded from .fam.
Ambiguous sex IDs written to friends.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 0.93359.
33499 variants and 154 people pass filters and QC.
Note: No phenotypes present.
Rozenns-MacBook-Pro:5-friends rozenn$ plink --file friends --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 friends
--genome
16384 MB RAM detected; reserving 8192 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (33499 variants, 154 people).
--file: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam
written.
33499 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 0.93359.
33499 variants and 154 people pass filters and QC.
Note: No phenotypes present.
IBD calculations complete.
Finished writing plink.genome .
Other method: use isoRelate to calculate IBD:
https://github.com/bahlolab/isoRelate/blob/master/vignettes/introduction.Rmd