User: gaelgarcia

gravatar for gaelgarcia
gaelgarcia100
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UK
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2 days, 2 hours ago
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3 years, 4 months ago
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Posts by gaelgarcia

<prev • 46 results • page 1 of 5 • next >
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Comment: C: Converting VCF to PLINK .bed binary fileset for pedigree checking with KING: How
... Does the information contained in the `.fam` file, or any pedigree/sample metadata information, actually go into the `.bed` file? Because if it doesn't... then I don't really need to worry about all of this - I could just create the .binary fileset from the VCF as instructed in the KING tutorial (w ...
written 6 days ago by gaelgarcia100
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Comment: C: Converting VCF to PLINK .bed binary fileset: How do the different tools availabl
... @chrchang: So in this case, if I run : `./plink2 --make-bed --vcf ~/path/to/mips.vcf.bgz --fam ~/path/to/mips_pedigree.fam --out mips` , then (if I understand correctly), `--make-bed` will output a `mips.fam` file identical to the `.fam` file passed with `--fam`? ...
written 10 days ago by gaelgarcia100
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Comment: C: retrospective trio analysis from WGS SNPs
... Thanks, Andrew. Yes, actually it looks like it uses all of them. (See https://www.biostars.org/p/313503/#313672) ...
written 10 days ago by gaelgarcia100
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Comment: C: get build 37 positions from dbSNP rsIDs
... You're right, it works. Who knows what I was doing that day... Thanks! ...
written 10 days ago by gaelgarcia100
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Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking for family relationships a priori?
... I'm trying to convert a VCF of ~15K samples (~4K families) into PLINK binary format to check for any pedigree errors using [KING][1]. > The input files need to be in PLINK binary format, e.g., ex.bed, > ex.fam, and ex.bim. There are [multiple tools][2] out there to convert a VCF to [PLINK bi ...
vcf fam gatk vcftools plink written 14 days ago by gaelgarcia100
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Comment: C: Is there a easy to use GATK pipeline for SNP calling?
... I agree - It would be awesome if GATK could be used through a front-end application or were more user-friendly! ...
written 14 days ago by gaelgarcia100
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Comment: C: SNP panel interrogated by KING for kinship estimation?
... Thanks, @chrchang523. By < covering the entire genome very well > , do you mean as long as they're spread out across the genome fairly evenly? We have sequencing data of a [very] targeted panel of genes across ~15K samples for which we're trying to do pedigree/sex checks. I'm trying to deter ...
written 16 days ago by gaelgarcia100
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Comment: C: Checking kinship coefficients and relationships and comparing genotyping data to
... Hi Dan, I'm trying to figure out what panel of SNPs KING interrogates to calculate kinship, but this doesn't seem to be explicitly stated anywhere. Do you know what this panel is? ...
written 16 days ago by gaelgarcia100
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Comment: C: Checking kinship coefficients and relationships and comparing genotyping data to
... Hi Steve, I'm trying to figure out what panel of SNPs KING interrogates to calculate kinship, but this doesn't seem to be explicitly stated anywhere. Do you know what this panel is? ...
written 16 days ago by gaelgarcia100
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Comment: C: Negative IBD values
... Hi Daniel, I'm trying to figure out what panel of SNPs KING interrogates to calculate kinship, but this doesn't seem to be explicitly stated anywhere. Do you know what this panel is? ...
written 16 days ago by gaelgarcia100

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