plink/seq Posts

Latest

Open

RNA-Seq

ChIP-Seq

SNP

Assembly

Tutorials

Tools

Jobs

Forum

Planet

All »

Home

Welcome to Biostar! about • faq • rss

Community

Log In

Sign Up

Add New Post

Showing selected topics • reset

or Classic search

votes

answers

1.0k

views

answers

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 3.4 years ago by spider_monkey • 10

votes

answer

2.0k

views

answer

Perl script for reformatting a plink/seq output file

perl plink/seq allele genotype reformat written 4.8 years ago by plink_9857 • 50

votes

answer

1.7k

views

answer

Loading IMPUTE2 dosage data into plink/seq

dosage plink/seq impute2 written 5.2 years ago by potassiumiodide0990 • 80 • updated 5.0 years ago by Vincent Laufer • 1.1k

Recent Votes

Recent Locations • All »

United States, 1 minute ago
Bloomington, USA, 2 minutes ago

Recent Awards • All »

Teacher to h.mon ♦ 30k
Scholar to h.mon ♦ 30k
Scholar to Kevin Blighe ♦ 63k
Appreciated to Istvan Albert ♦♦ 84k
Teacher to Bastien Hervé ♦ 4.7k
Scholar to Bastien Hervé ♦ 4.7k

Recent Replies

C: Tools to filter the heterozygous SNPs with biased allele depth (AD) values in vc by michaeldonaldson • 10
Hi Pierre, Can you clarify how the above script relates to allele balance (i.e., the proportion ...
C: nr database "No alias or index file found for protein database" by genomax ♦ 87k
With new default blast+ `v5` database, size of the files changed (individual files are now larger...
C: FastqToSam (Picard) syntax paired-end reads by h.mon ♦ 30k
Yes, but this splitting of files is uncommon nowadays. This was common when files were often tran...
C: EdgeR and contrasts: How to compare with a group not in the model by h.mon ♦ 30k
No, not when you set the intercept to zero. Even if the intercept isn't set to zero, one needs ...
A: ObjTables: tools for creating and reusing high-quality spreadsheets (e.g., suppl by jonrkarr • 60
Table Schema (Frictionless Data) is probably one of the closest general-purpose tools. Other simi...
C: Variant Quality Score Recalibration (Vqsr) For Non-Human Genomes by Begonia_pavonina • 20
Hello Jeremy, I had the same question than Tonyzeng and was wondering how I could filter my varia...
A: Publicly Available WGS Samples for Panel of Normals? by tjbencomo • 0
I ended up using the hg38 1000 Genomes PON from the Broad linked to by @RamRS. Although the PON w...
C: ObjTables: tools for creating and reusing high-quality spreadsheets (e.g., suppl by Jeremy Leipzig ♦ 19k
This looks super interesting. Can you compare ObjTables to Frictionless Data?
C: Query a public sql server from within python by genomax ♦ 87k
Can you do this as a subprocess/system call ([LINK][1])? [1]: https://stackoverflow.com/quest...
C: Adding gene set to GSVA by igor ♦ 11k
The problem is you are trying to convert it to a `GeneSetCollection` object. You don't need to do...
C: DE analysis with limma (What to include in the model?) by Davide • 10
I agree on the points Kevin is making. What are the DEG after using "adjusted p-values" for both ...
C: How to analyze Illumina RNASeq data by Manoj • 50
Hi, I am trying following command, however it is showing error. Please correct me, I am pretty ne...

Content

Help

About
FAQ

Access

RSS
Stats
API

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Traffic: 1426 users visited in the last hour