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Correct bash command to zip your vcf file

biogeek — Wed, 04 Mar 2020 04:32:17 -0600

bgzip -c file.vcf > file.vcf.gz
tabix -p vcf file.vcf.gz

#More at http://www.htslib.org/doc/tabix.html

Bash oneliner to extract all ids from a multifasta file

biogeek — Tue, 18 Feb 2020 08:06:09 -0600

#List of ids - one per line in allIds.txt

$ awk 'BEGIN{while((getline<"allIds.txt")>0)l[">"$1]=1}/^>/{f=!l[$1]}f' seq.fa

# You can play with this f=!l[$1 ] if wanted to extract or not extract the ids

Install snakemake and activate on conda

biogeek — Tue, 18 Feb 2020 06:33:24 -0600

$ conda create -c bioconda -c conda-forge -n snakemake snakemake
$ conda activate snakemake