User: QVINTVS_FABIVS_MAXIMVS

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There's more than one way to hunt a CNV

Posts by QVINTVS_FABIVS_MAXIMVS

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SNP + INDEL Merging Guidelines
... Say I have SNP INDEL calls for 1000 individuals. These 1000 samples were joint-called and recalibrated with GATK in 10 batches. As a result I have 10 VCF files with SNP and INDEL calls that I would like to merge. I only have access to the VCF files, so re-calling from the BAMs is not an option. ...
vcf indel snp merging written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.1k
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Comment: C: When should you left-align INDELs (and why?)
... Thanks for the clear answer. Do you recommend `vt` or `bcftools` for normalization? ...
written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.1k
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Comment: C: When should you left-align INDELs (and why?)
... Edited the main query above. ...
written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.1k
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When should you left-align INDELs (and why?)
... Say I have two VCFs with 100 samples in each file. Each VCF was joint-called separately and now I want to merge the variant calls. Do I need to left-align the INDELs in the merged VCF? I've used `bcftools norm` in the past and got odd results. It seems that `vt` is a better tool for this. Is lef ...
indel vcf left align written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.1k
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Answer: A: How do I interpret alternative allele <CN2> for structural variants in 1000 geno
... It's like this For CNVs the REF is `` Humans are diploid thus : `0/0` == `CN1/CN1` or 2 copies --- Say the ALT is `` * `0/0` = CN1/CN1 = 2 copies * `0/1` = CN1/CN0 = 1 copy * `1/1` = CN0/CN0 = 0 copies --- With multiallelic variants the order of the alleles is the same as the genotypes (i ...
written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.1k
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Recalculate QUAL for SNPs in VCF
... I have joint called VCFs that I have split into respective pedigrees. Due to the nature of a software I'm using, I need to recalculate the QUAL scores for the pedigree VCFs. I read on these forums that bcftools is able to do this, however the post has no clear answer https://www.biostars.org/p/1 ...
vcf haplotype caller snv snp written 4 months ago by QVINTVS_FABIVS_MAXIMVS2.1k
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Comment: C: Recalculate QUAL and INFO fields for a subset of samples in a VCF
... what is the command? ...
written 4 months ago by QVINTVS_FABIVS_MAXIMVS2.1k
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Comment: C: Count SNPs per individual FAST!
... Either IID #UNIQUE_ALLELES Or IID #UNIQUE_ALLELES #ALT_ALLELES so the first file would output `ID1 1` for `1/1` genotype but the second file you have `ID1 1 2` ...
written 4 months ago by QVINTVS_FABIVS_MAXIMVS2.1k
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Count SNPs per individual FAST!
... Say I have a large (N samples > 2000) VCF or plink bed file. What's the quickest way to calculate the number of alleles (unique alleles and # ALT genotypes) for each sample? What are the options that can quickly digest a 1Tb VCF (broken by chrom)? Plink is ridiculously fast for this, but I do ...
gwas plink snp written 4 months ago by QVINTVS_FABIVS_MAXIMVS2.1k • updated 4 months ago by chrchang5233.9k
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Comment: C: Random Forest returns "New factor levels not present in the training data"
... I figured it out. The VCFs I was working on had different Tranche levels. So it was a factor that was not trained on ...
written 5 months ago by QVINTVS_FABIVS_MAXIMVS2.1k

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