User: rshoobs

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rshoobs0
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Posts by rshoobs

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Does bcftools support any kind of large dictionary based editing of variants?
... I have a text file of snp positions that change between builds and would like to update my vcf file accordingly. I could throw the whole thing into R, but I'd like to know if bcftools has anything more convenient. Essentially I am looking for something that interfaces with the output of liftOver in ...
bcftools snp written 24 days ago by rshoobs0 • updated 24 days ago by Pierre Lindenbaum121k
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will recombination rates differ between builds of the human genome?
... I am running MOSAIC which requires something akin to recombination rate as part of their input, however my data is in a different build than their example data. Will the recombination rates change between builds of the human genome? Or can i use their provided data for my purposes? If not how can i ...
genome recombination written 25 days ago by rshoobs0 • updated 25 days ago by h.mon26k
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calculating cumulative recombination rate for MOSAIC?
... I am running MOSAIC and don't understand how their "cumulative recombination rate" is calculated. I have the 1000G genetic map that their data appears to be based off of, but don't know how to convert the combined rate to the cumulative rate. As an example the first few lines of the genetic map look ...
mosaic local ancestry recombination written 25 days ago by rshoobs0
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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 5 months ago by rshoobs0 • updated 4 months ago by Biostar ♦♦ 20
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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 7 months 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 7 months 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 9 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 9 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 9 months ago by rshoobs0

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