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Individual IDs in .vcf format are not the same as in the original plink format that I converted to .vcf using plink/seq

vcf plink/seq .bed plink convert file format written 2.5 years ago by spider_monkey • 10

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Perl script for reformatting a plink/seq output file

perl plink/seq allele genotype reformat written 4.0 years ago by plink_9857 • 50

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1.5k

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Loading IMPUTE2 dosage data into plink/seq

dosage plink/seq impute2 written 4.3 years ago by potassiumiodide0990 • 80 • updated 4.1 years ago by Vincent Laufer • 1.1k

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Recent Replies

C: is 0-based start and 1-based end of bed format not compatible with htseq-count? by colin.kern • 420
Why do you say that htseq is 0-based, open ended? Since it takes a GFF as input, I would expect i...
A: How to download large amount of data from NCBI? by Brice Sarver • 2.9k
It looks like you're getting some [good information on your same reddit post][1], and my personal...
C: Link pathways to Gene Onthologies from RNA-seq differential expressed genes by jared.andrews07 • 3.1k
Does it give you any sort of identifier for the pathway besides the name? There may be a way to l...
A: where to download mm9.fa masked? by Michel Edwar • 70
lol :) funny Thanks, I will try it.
C: where to download mm9.fa masked? by WouterDeCoster ♦ 40k
No, mouse!
C: Import VCF from GnomAD by tpoterba • 50
Also, if you're running this on Google Cloud Dataproc, the bucket identifier should start with `g...
C: Import VCF from GnomAD by tpoterba • 50
You should also know that the gnomAD team has files available already in Hail native format, from...
C: where to download mm9.fa masked? by Pierre Lindenbaum ♦ 123k
[cat][1] ? [1]: http://man7.org/linux/man-pages/man1/cat.1.html
C: Clipping primer after alignment by michael.ante • 3.4k
Hi finswimmer, A possible solution is to convert your BAM file into BED format and use `bedtools...
C: How to solve the different number of hits from tblastn when I use the option -pa by carina2817 • 0
I don't get any warning message
A: To Cloud or Not to Cloud - Privacy implications of genetic data sharing by anneykim • 0
My research at MIT CSAIL with Professor Manolis Kellis has actually made a pretty neat tool for p...
A: Why Is Snp Data Generally Restricted? by anneykim • 0
I've also experienced a lot of frustration getting access to SNP data. My research at MIT CSAIL ...

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