User: cetin.m

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cetin.m20
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Posts by cetin.m

<prev • 17 results • page 1 of 2 • next >
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Relatedness: Calculating k0, k1 and k2
... I want to calculate relatedness between two individuals. Suppose that I am looking at 3 loci: Ind.1: 0/0, 0/1, 1/1 Ind 2: 0/1, 0/1, 0/0 How can I calculate k0, k1 and k2? ...
relatedness written 22 days ago by cetin.m20
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How to calculate IBD
... I am trying to understand how IBD calculations are done based on SNPs. I haven't been able to grasp the subject even though I looked at several papers. I am hoping by looking at a simple case someone could show me how it is done. Assume there is a locus and two individuals. They may or may not b ...
ibd written 8 weeks ago by cetin.m20 • updated 7 weeks ago by Charles Warden6.5k
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Can't determine any relatedness using lcMLkin
... Does anyone here use the software lcmlkin for relatedness estimation? I am having some trouble and would like to ask some questions. ----- EDIT: Basically, I can't determine any relatedness between individuals who I know are related. (the CEPH family) I am using the CEU population in 1000G as ...
lcmlkin written 8 weeks ago by cetin.m20 • updated 8 weeks ago by Santosh Anand4.7k
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IBD probablity for each Genotype pair
... I am trying to understand the below table from the lcmlkin paper, (Lipatov 2015). It shows the genotype pairs and the probabilities of having 0, 1 and 2 IBD alleles for each of 4 pairs. Maybe not the best place to ask, but can someone please help me understand where these probabilities come fro ...
relatedness lcmlkin written 8 weeks ago by cetin.m20
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Beagle permanent file
... I am running Beagle for imputation. I am in the process ofoptimizing it, so I have to run the program repeatedly with slightly different parameters. But I am using the same reference panel each time. I am wondering if the calculations made on this reference panel can be permanently written to the h ...
imputation beagle written 10 weeks ago by cetin.m20
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Comment: C: Beagle 4.1 imputation
... It is a server with 200BG ram. and here is the cpu: Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit CPU(s): 32 Thread(s) per core: 2 Core(s) per socket: 8 Socket(s): 2 Model name: Intel(R) Xeon(R) CPU E5-2640 v2 @ 2.00GHz CPU M ...
written 10 weeks ago by cetin.m20
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bcftools 1.4.1 call parameters
... 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 bcf with at least two different commands: bcftools call -mV indels bcftools call -c -v I get two vastly different results wi ...
bcftools call snp written 11 weeks ago by cetin.m20 • updated 11 weeks ago by finswimmer11k
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Answer: A: Fst calculation between my own population and 1000 genome populations
... When I did something similar I used a python code which did not involve merging the files. ...
written 12 weeks ago by cetin.m20
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Beagle 4.1 imputation
... I am running Beagle 4.1 to impute SNPs in human WGS data. I ran chr 21 and it took 10 days. (with ~1M markers in the ref panel) That means the whole genome would take 2 years.. How do other people manage this? ...
imputation written 12 weeks ago by cetin.m20 • updated 9 weeks ago by Biostar ♦♦ 20
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Comment: C: Choice of ref. Genomes
... Thanks!! Where can I find more information about how GRCh 38 was assembled? I did google but no find. ...
written 3 months ago by cetin.m20

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