User: cetin.m

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cetin.m30
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Posts by cetin.m

<prev • 20 results • page 1 of 2 • next >
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Comment: C: GATK multi sample variant calling
... Makes a lot of sense! ...
written 6 weeks ago by cetin.m30
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GATK multi sample variant calling
... I am trying to call SNPS from two bam files simultaneously. I want it to be written to the same vcf, with one column for each sample. I run the following command: > ./GenomeAnalysisTK.jar -T UnifiedGenotyper -I **sampleA.bam** -I > **sampleB.bam** > -R /mnt/NEOGENE1/share/ref/genomes/hsa ...
variant calling gatk snp written 6 weeks ago by cetin.m30
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ANGSD vs GATK for genotype likelihoods
... Hello, Can anyone please comment on advantages and disadvantages of ANGSD vs GATK for getting genotype likelihoods? Our samples are low coverage. And our goal is to do imputation after this step. Any comments greatly appreciated. ...
gatk genotype likelihoods angsd written 3 months ago by cetin.m30
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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 6 months ago by cetin.m30
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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 7 months ago by cetin.m30 • updated 7 months ago by Charles Warden7.2k
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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 7 months ago by cetin.m30 • updated 7 months ago by Santosh Anand4.9k
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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 7 months ago by cetin.m30
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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 8 months ago by cetin.m30
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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 8 months ago by cetin.m30
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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 8 months ago by cetin.m30 • updated 8 months ago by finswimmer12k

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