User: markgodek

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markgodek30
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Posts by markgodek

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Comment: C: How to add rsIDs to VCF?
... gatk VariantAnnotator -R '/home/mark/Desktop/Reference_Genome_hg19/hg19.fa' -I '/home/mark/Desktop/Google_CEPH_Genomes_hg19/platinum-genomes_bam_NA12877_S1.bam' -V '/home/mark/Desktop/CEPH VCFs/platinum-genomes_vcf_NA12877_S1.genome.vcf.gz' -O '/home/mark/Desktop/CEPH VCFs/GATK_NA12877_S1_rsids. ...
written 11 months ago by markgodek30
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How to add rsIDs to VCF?
... I'm still a beginner and using [Illumina Platinum Genomes as a toy dataset][1]. Google supplies the files in VCF, but I need them annotated with rsIDs. I've tried GATK VariantAnnotator and bcftools annotate [as suggested by this post I found via Google][2] and [this Biostars post][3], but I'm not h ...
snp written 11 months ago by markgodek30 • updated 8 months ago by erkinacar520
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Comment: A: 1000genomes data to 23&me format.
... I've been looking into analyzing open data with GEDmatch's tools for my thesis project for a few months. You should be [able to get genotypes for a specific population from the VCF files on 1000 Genomes Project.][1] If you are committed to using the files from Globus, you will have to do SNP calli ...
written 11 months ago by markgodek30

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Popular Question 10 months ago, created a question with more than 1,000 views. For How to add rsIDs to VCF?

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