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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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converting 23andme v5 format to VCF format #1243

Closed jkotl0327 closed 4 years ago

jkotl0327 commented 4 years ago

Hello, I downloaded your source code (in mac terminal, bash shell) using the simple copy-paste command you offered. I then pointed the environment label to the proper location by copying and pasting the command on your website. Then I entered your command to convert my 23andme file into VCF format: 'bcftools convert --tsv2vcf input.tab.gz -f ref.fa -s Jeremy -Ob -o JeremyDNA.bcf' At this point I got: 'bcftools: command not found' What should I do? I have attached 3 screenshots of everything I did below. Thank you.

Screen Shot 2020-06-14 at 10 32 40 PM Screen Shot 2020-06-14 at 10 32 52 PM Screen Shot 2020-06-14 at 10 33 14 PM
freeseek commented 4 years ago

You have to copy the bcftools binary inside a directory in your binary path or, alternatively, invoke the command as ./bcftoools rather than as bcftools while making sure it is located in the same directory where you are running the shell command

pd3 commented 4 years ago

Also note that the command export BCFTOOLS_PLUGINS must have the proper directory set. You can't just blindly copy and paste it, unless the path /path/to/bcftools/plugins exists.