VCFtools calculate SNP density

Question

[christinachavez]

I am attempting to use VCFtools to calculate snp densities of specific genes within a VCF from the Exac Browser. Here is the script that I am using:

vcftools --vcf ExAC.r0.3.1.sites.vep.vcf --chr chromosome_# --from-bp start_coordinate --to-bp end_coordinate --SNPdensity gene_size --out gene_name

--SNPdensity should take the positions I give it, and calculate the SNP density from the gene_size I give it, but my output files are inconsistent. VCFtools seems to be calculating the SNP density but not for the entire region I give it, and I end up with two different SNP densities for outputs.

Has anyone had this issue and figured out how to fix it?

[ahusnoo]

@christinachavez Have you been able to find a solution as I have to do something similar too?

Answer 1

[ashishbansal12300]

These options are used to specify the input and output files.

INPUT FILE OPTIONS

--vcf <input_filename>

This option defines the VCF file to be processed. VCFtools expects files in VCF format v4.0, v4.1 or v4.2. The latter two are supported with some small limitations. If the user provides a dash character ’-’ as a file name, the program expects a VCF file to be piped in through standard in.

--gzvcf <input_filename>

This option can be used in place of the --vcf option to read compressed (gzipped) VCF files directly.

--bcf <input_filename>

This option can be used in place of the --vcf option to read BCF2 files directly. You do not need to specify if this file is compressed with BGZF encoding. If the user provides a dash character ’-’ as a file name, the program expects a BCF2 file to be piped in through standard in.

OUTPUT FILE OPTIONS

--out <output_prefix>

This option defines the output filename prefix for all files generated by vcftools. For example, if <prefix> is set to output_filename, then all output files will be of the form output_filename.*** . If this option is omitted, all output files will have the prefix "out." in the current working directory.

--stdout 
-c

These options direct the vcftools output to standard out so it can be piped into another program or written directly to a filename of choice. However, a select few output functions cannot be written to standard out.

--temp <temporary_directory>

This option can be used to redirect any temporary files that vcftools creates into a specified directory.