I personally have never compared inbreeding coefficients between SNPs and indels. I would have expected the values to be different (i.e., probably different mutation equilibrium for indels compared to SNPs) but similar at the same time. One thing to think about is whether the SNPs and indels you are comparing are di-allelic (two alleles) or multi-allelic (more than two alleles). For theory, I would have to do a literature search.
I'm really confused of the terms kinship coefficient coefficient of relationship relatedness inbreeding coefficient As I understood, inbreeding coefficient shows how much an individual's parents …
I first do samtools mpileup: samtools mpileup -uf /mnt/NAS/share/Ref/human/hs37d5.fa -l 1000G.bed -q 30 -Q 30 in.bam -o out.bcf Then: I can call snps from the …
I'm using Annovar for variant annotation I want to input a vcf file and I get this warning message: #perl convert2annovar.pl Indel_Autoss.vcf -format vcf4 > …
Hi I'm working with Indels filtered using GATK best practices, I got a vcf, converted to plink and calculated the heterozygosity frequency using plink function …
<p>I am currently preprocessing data from the Illumina PsychArray chip. This chip includes normal tag SNPs and well as other genetic variants such as indels.</p> …
I personally have never compared inbreeding coefficients between SNPs and indels. I would have expected the values to be different (i.e., probably different mutation equilibrium for indels compared to SNPs) but similar at the same time. One thing to think about is whether the SNPs and indels you are comparing are di-allelic (two alleles) or multi-allelic (more than two alleles). For theory, I would have to do a literature search.
Thank you for your response. They are di-allelic (SNPs and Indels). I will do a literature research to see what I can find.