User: rshoobs

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rshoobs0
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Posts by rshoobs

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alternative chromosomes in liftover, what does this mean?
... I've been performing liftover from hg19 to hg38 based on genetic position using the LiftOver utility. I have several snps the chromosomes of which have been labelled as such `chr7_KI270803v1_alt`. In particular chromosomes 7 and 8 demonstrate an inordinate amount of this tagging. On further inspecti ...
genome snp written 9 days ago by rshoobs0
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Comment: C: Liftover errors with CrossMap and Picard
... I've been trying further and find that it works with a bed file that I've created from my vcf. Only issue is that It doesn't preserve any mapping so i can't coordinate any genotypes! ...
written 10 weeks ago by rshoobs0
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Liftover errors with CrossMap and Picard
... Hi all, I am attempting to use CrossMap to convert my dosage files output from the sanger imputation service from hg19/37 to hg38. Here is the command I am using python3 ~/software/CrossMap-0.3.1/bin/CrossMap.py vcf ~/Data/liftover/hg19ToHg38.over.chain.gz 22_withMAF.vcf.gz ~/Data/GenCode/GRC ...
software error rna-seq snp written 10 weeks ago by rshoobs0
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Comment: C: Calculate minor allele frequency from VCF
... yes this is perfect! has a MAF option I can use ...
written 3 months ago by rshoobs0
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Calculate minor allele frequency from VCF
... Hi All! I have sanger imputed genotype files and want to filter them based on MAF. Unfortunately they do not contain MAF scores. Is there an easy way to calculate MAF from this file? For reference here is an exmaple of what it does contain: #CHROM POS ID REF ALT QUAL FILTE ...
genome snp written 3 months ago by rshoobs0
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Sanger imputation assigns some empty SNP IDs, Is this normal?
... Hi all! I recently performed some imputation using the sanger imnputation service. While I was parsing the data I noticed that some of the SNP IDs it outputs are filled with a period '.' rather than an actual ID. for reference the output looks somewhat like this ##header info ##header in ...
vcf sanger imputation written 3 months ago by rshoobs0

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