SNP calling without bcftools and vcftools

Question

[ongchip]

Hello, I am trying to analyze my data with this method: https://www.ebi.ac.uk/sites/ebi.ac.uk/files/content.ebi.ac.uk/materials/2014/140217_AgriOmics/dan_bolser_snp_calling.pdf

I made bcf files with "samtools mpileup" command. However, both bcftools and vcftools are not installed in the server computer. I tried to install on the server, but the error occurs: -bash: /usr/bin/yum: /usr/bin/python: bad interpreter: Permission denied

It seems I have no permission to install using yum. Is there another way to analyze SNPs with only samtools except for bcftools and vcftools?

[Pierre Lindenbaum]

but the error occurs: -bash: /usr/bin/yum: /usr/bin/python: bad interpreter: Permission denied

that's very strange. How do you compile ? what is the command line ? what are the messages before the error ?

Is there another way to analyze SNPs with only samtools except for bcftools and vcftools?

gatk haplotypecaller, but IMHO you'd better solve the problem above.

[ongchip]

The package libcurl-devel is required to install bcftools. However, when I install libcurl-devel with this command:

yum install libcurl-devel

then the error occurs:

-bash: /usr/bin/yum: /usr/bin/python: bad interpreter: Permission denied

[jkbonfield]

That method is very outdated. It uses samtools to generate VCF, which is no longer supported. Plus it has bcftools for the calling, which is completely at odds with "SNP calling without bcftools and vcftools"!

If you do want to use samtools / bcftools, then it's probably best to follow the protocol published there:

http://www.htslib.org/workflow/wgs-call.html

Answer 1

[colindaven]

You didn't write much about what really went wrong, what you server is etc, and if you are supposed to have admin rights, or any command.

But I would recommend conda for installing software like this in the user space, and many agree here.

Here is a nice tutorial to get started:

Greatly speed up conda by using mamba

and bioconda package list:

https://anaconda.org/bioconda/repo