User: wangdavid758

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wangdavid75820
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Posts by wangdavid758

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wget UCSC Table Browser
... How can I download UCSC Table Browser data using wget or any command line tool. I need to download it on a computing cluster that doen't have a UI. ...
table browser wget ucsc written 5 months ago by wangdavid75820 • updated 5 months ago by Pierre Lindenbaum115k
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Comment: C: Converting Illumina Omni 1 Quad v1.0 to hg19
... I believe it's position 882858 on hg18. Still not quite right. If you look it up on dbsnp (https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=13303227), there are some sources in the records section that have the position I specified. Do you happen to know what these are? ...
written 7 months ago by wangdavid75820
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Comment: C: Converting Illumina Omni 1 Quad v1.0 to hg19
... For reference, a SNP with rsID such as rs13303227 has position 882608 in my file but has position 892745 in hg19. ...
written 7 months ago by wangdavid75820
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Converting Illumina Omni 1 Quad v1.0 to hg19
... I have data from a Illumina Omni Quad 1 v1.0 array and need to convert this to hg19/GRCh37. The easiest way I know of is to use the strand files from here: http://www.well.ox.ac.uk/~wrayner/strand/sourceStrand/index.html However, the file has already been preprocessed so the cnv IDs that are requi ...
genome build conversion written 7 months ago by wangdavid75820
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Extract SNPs by position from gvcf
... I have 10 gvcfs for 10 samples and a list of SNP positions (chr# and position) I want to extract from the gvcfs. I can't just use vcftools to do this because the position is given as a range (start position and end position) in the gvcf and if the position in my list is within the range but not the ...
extract position snp gvcf written 8 months ago by wangdavid75820 • updated 8 months ago by Pierre Lindenbaum115k
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Merging vcf files (intersection and union)
... How can I merge 2 vcf files, each with multiple samples, the so the final file has all the samples but the intersection of the SNPs. How about union on the SNPs? ...
vcf merge written 8 months ago by wangdavid75820 • updated 5 months ago by ami23.sarr0
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Can you assume variants not in VCF are all monomorphic for the reference allele?
... I have a VCF file, lets call it file A, which was created by performing variant calling using GATK on whole genome sequencing data. For SNPs that do no appear in the VCF, can I assume that the SNP is monomorphic for the reference allele (i.e all 0 encoding). Note that sites that are monomorphic for ...
vcf variant calling imputation missing variants written 9 months ago by wangdavid75820 • updated 9 months ago by Pierre Lindenbaum115k
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Recode vcf with specified reference allele
... Hi, I have a phased vcf file and I want to recode the reference allele according to be what is a specified in a list. The list is 2 columns: SNP id in the first, and the reference allele I want in the second. For example, if my REF and ALT alleles in the vcf are A and T respectively for SNP rs12345 ...
vcf vcftools plink flip reference allele written 12 months ago by wangdavid75820 • updated 12 months ago by Pierre Lindenbaum115k

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