User: cetin.m

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cetin.m50
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Posts by cetin.m

<prev • 24 results • page 1 of 3 • next >
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Bcftools Mpileup bias for alternative alleles?
... I have called snps from a bam file using the below commands: /usr/local/sw/bcftools-1.9/bcftools mpileup -f /mnt/NEOGENE2/share/ref/genomes/hsa/hs37d5.fa -I /mnt/NEOGENE2/share/dna/hsa/comparative_seqs/lazaridis2014/Loschbour.hg19_1000g.dq.bam.hs37d5.fa.cons.90perc.bam -R /mnt/NAS/projects/2018 ...
gatk bcftools mpileup snp written 12 weeks ago by cetin.m50 • updated 12 weeks ago by Kevin Blighe63k
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Comment: C: Plink --freq function
... Yes I see the positions there. But I don't know how to replace the rs IDs with them. ...
written 7 months ago by cetin.m50
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Plink --freq function
... I have a set of files, with the names yripublished.bed, yripublished.bim, yripublished.fam I got the frequencies of SNPs in these files with the following command: /usr/local/sw/plink-1.90/plink --bfile yripublished --bed yripublished.bed --freq This gives an output, where each SNP is defined ...
plink written 7 months ago by cetin.m50 • updated 5 months ago by chrchang5237.1k
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Can someone provide me with vcf files with X and Y chromosomes? (Human)
... I want to run a simulation using vcf files. It needs to contain sex chr. I think sex chromosome variant calling is not straightforward. And publications usually put Bam or Fastq. So I was wondering if someone could provide me with vcf files with X and Y chromosomes? ...
vcf sex chr written 9 months ago by cetin.m50 • updated 9 months ago by Kevin Blighe63k
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Comment: C: GATK multi sample variant calling
... Makes a lot of sense! ...
written 12 months ago by cetin.m50
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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 12 months ago by cetin.m50
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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 14 months ago by cetin.m50
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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 17 months ago by cetin.m50
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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 18 months ago by cetin.m50 • updated 18 months ago by Charles Warden7.8k
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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 18 months ago by cetin.m50 • updated 18 months ago by Santosh Anand5.1k

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Popular Question 6 months ago, created a question with more than 1,000 views. For Full genome phyloP scores from UCSC Browser

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