Question: problem with installing and running bcftools
0
gravatar for rotemkat
5 months ago by
rotemkat0
rotemkat0 wrote:

I tried to follow the instructions here: https://samtools.github.io/bcftools/ being in the following path - /Users/my_username - i followed the commands and indeed now i have the bcftools folder.

Then, I want to filter my VCF file, so I did the following: (based on the instructions here: https://samtools.github.io/bcftools/howtos/variant-calling.html)

cd bcftools

bcftools filter -i'%contig==1' path_to_my_file/my_file.VCF | bcftools stats | grep TSTV

but i get the following error:
-bash: bcftools: command not found

what am I doing wrong?...

Thanks !!!

bcftools vcf • 243 views
ADD COMMENTlink modified 5 months ago by finswimmer13k • written 5 months ago by rotemkat0
3

its a classical PATH problem: http://www.linfo.org/path_env_var.html

./bcftools filter
ADD REPLYlink modified 5 months ago • written 5 months ago by Pierre Lindenbaum129k

I still get multiple errors =/

$ ./bcftools filter -i 'CHROM==1' /path/file.vcf | bcftools stats | grep TSTV

-bash: bcftools: command not found
[W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
Error: cannot use arithmetic operators to compare strings and numbers
ADD REPLYlink modified 5 months ago by genomax85k • written 5 months ago by rotemkat0

I don't think you read the link above about what is a PATH.

$ ./bcftools filter -i 'CHROM==1' /path/file.vcf | ./bcftools stats | grep TSTV
ADD REPLYlink written 5 months ago by Pierre Lindenbaum129k
0
gravatar for onestop_data
5 months ago by
onestop_data260
onestop_data260 wrote:

Alternatively, you could use Bioconda and install it in your os path.

ADD COMMENTlink written 5 months ago by onestop_data260
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