Fnyasimi
/ BCFtools cheat sheet
Created
January 10, 2023 20:08
— forked from elowy01/BCFtools cheat sheet
BCFtools cheat sheet
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| *bcftools filter | |
| *Filter variants per region (in this example, print out only variants mapped to chr1 and chr2) | |
| qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz | |
| *printing out info for only 2 samples: | |
| bcftools view -s NA20818,NA20819 filename.vcf.gz | |
| *printing stats only for variants passing the filter: | |
| bcftools view -f PASS filename.vcf.gz |
Fnyasimi
/ compare_expression.R
Last active
March 30, 2022 19:04
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| #! /usr/bin/env Rscript | |
| suppressWarnings(suppressMessages(library(dplyr))) | |
| fn_remove_ver_from_names = function(df) | |
| { | |
| ind = substr(names(df),1,4) == "ENSG" | |
| names(df)[ind] = substr(names(df)[ind],1,15) | |
| df | |
| } |