User: bsmith030465

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bsmith030465150
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Posts by bsmith030465

<prev • 56 results • page 1 of 6 • next >
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Comment: C: PLINK : Error: --tdt requires a case/control phenotype.
... Ah, my mistake!! Thanks, that worked! ...
written 8 days ago by bsmith030465150
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PLINK : Error: --tdt requires a case/control phenotype.
... Hi, I was trying to run an analysis: > plink --bfile my.samples --tdt but get the following error: Error: --tdt requires a case/control phenotype. The corresponding family file seems to be okay (i.e. case/control status looks ok): MJ19 ID55 ID57 ID56 2 2 MJ19 ID56 0 0 ...
plink written 8 days ago by bsmith030465150 • updated 8 days ago by chrchang5235.5k
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PLINK - error in --make-bed
... Hi, I was trying to convert my ped file to a bed file with the command plink --file mysamples --make-bed However, I get the error: Scanning .ped file... Possibly irregular .ped line. Restarting scan, assuming multichar alleles. Error: Half-missing call in .ped file at varia ...
plink written 8 weeks ago by bsmith030465150 • updated 8 weeks ago by chrchang5235.5k
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Comment: C: PLINK: filter for indels
... Thanks for the help and explanation. That worked! Much appreciated. ...
written 3 months ago by bsmith030465150
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Comment: C: PLINK: filter for indels
... I am trying to exclude the 'range' of snps with this file format. plink --bfile myfile --exclude snp.pos.txt --range --out myfile.indels --make-bed but it says " Note: --range flag deprecated. Use e.g. '--extract range [filename]'." It also gives an error if I use: plink --bfile myfile ...
written 3 months ago by bsmith030465150
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Comment: C: PLINK: filter for indels
... Since my variants IDs weren't unique, I did some file processing to my snps output file (myfile.snps above) and got the snp ids that I want to exclude ('snp.pos.txt'): 1 10101 10101 10101 1 10493 10493 10493 1 10560 10560 10560 1 11994 11994 11994 . . and then I ran plink ...
written 3 months ago by bsmith030465150
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PLINK: filter for indels
... Hi, How do I filter my plink files so that only indels are kept? I used the following command to keep only snps: plink --bfile myfile --snps-only --out myfile.snps Which command/option should I use to retain only indels? Thanks ...
plink written 3 months ago by bsmith030465150 • updated 3 months ago by zx87547.9k
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gnomAD: query utilitites
... Hi, I wanted to query the gnomAD database without having to download and configure the entire data. Is there a way gnomAD provides an API for programmatic access? For example, for a given variant id, I want to retrieve the Total 'Allele Count': INPUT: '1-978628-C-T' (or 'rs116586548') OUTP ...
gnomad written 4 months ago by bsmith030465150 • updated 4 months ago by Garan580
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PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
... Hi, I am trying to convert a vcf.gz file to bed/bim/fam format using PLINK2 (data is hg38). My command is: plink2 --vcf variants.vcf.gz --out variants --freq --make-bed --chr 1-22 XY I get an error: Error: Invalid chromosome code 'chr11_KI270721v1_random' on line 36088290 of How can I ...
vcf plink written 5 months ago by bsmith030465150 • updated 5 months ago by chrchang5235.5k
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Comment: C: samtools fastq compression
... file Sample_R1.fastq.gz Sample_R1.fastq.gz: gzip compressed data, from Unix, max speed ...
written 10 months ago by bsmith030465150

Latest awards to bsmith030465

Great Question 8 weeks ago, created a question with more than 5,000 views. For PLINK: Convert bed,bim, fam to vcf file
Popular Question 3 months ago, created a question with more than 1,000 views. For PLINK: merge .bed files
Popular Question 3 months ago, created a question with more than 1,000 views. For biomaRt: getBM & getSequence
Great Question 10 months ago, created a question with more than 5,000 views. For PLINK: merge .bed files
Epic Question 10 months ago, created a question with more than 10,000 views. For PLINK: merge .bed files
Popular Question 10 months ago, created a question with more than 1,000 views. For PLINK: merge .bed files
Popular Question 16 months ago, created a question with more than 1,000 views. For PLINK: Change affection status
Popular Question 20 months ago, created a question with more than 1,000 views. For GRanges intersect operation
Great Question 2.3 years ago, created a question with more than 5,000 views. For PLINK: merge .bed files
Popular Question 2.3 years ago, created a question with more than 1,000 views. For GRanges intersect operation
Popular Question 2.3 years ago, created a question with more than 1,000 views. For PLINK: Change affection status
Popular Question 2.3 years ago, created a question with more than 1,000 views. For PLINK: merge .bed files
Popular Question 2.3 years ago, created a question with more than 1,000 views. For biomaRt: getBM & getSequence
Popular Question 2.3 years ago, created a question with more than 1,000 views. For PLINK: Change affection status
Great Question 2.7 years ago, created a question with more than 5,000 views. For How To Determine The Statistical Significance Of Overlap (Intersect) Between Three Sets
Popular Question 2.7 years ago, created a question with more than 1,000 views. For PLINK: Change affection status
Popular Question 2.7 years ago, created a question with more than 1,000 views. For PLINK: merge .bed files
Popular Question 3.0 years ago, created a question with more than 1,000 views. For PLINK format to EIGENSTRAT format
Popular Question 4.1 years ago, created a question with more than 1,000 views. For PLINK format to EIGENSTRAT format
Popular Question 4.1 years ago, created a question with more than 1,000 views. For PLINK: Convert bed,bim, fam to vcf file
Student 6.4 years ago, asked a question with at least 3 up-votes. For How To Determine The Statistical Significance Of Overlap (Intersect) Between Three Sets

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