Useful external tools

Useful bcftools commands

Collapse multiple lines with the same genomic position into a single line

bcftools norm -m +any [-O <output_format> -o <output>] <input_file>

Output format can be one of the following strings: "z" (compressed VCF),"b" (compressed BCF) or "bu" (uncompressed BCF). If nothing is specified, the default is uncompressed VCF. If the -o parameter is omitted, the output is printed to stdout.

Producing block compressed VCFs/BCFs

bcftools view [-O <output_format> -o <output>] <input_file>

The output file name should ideally end with the suffix ".[vcf|bcf].gz".

Generating the index for a block compressed VCF/BCF file

bcftools index [-f] <file>

The above command will create a CSI index. To produce a tabix index:

bcftools index [-f] -t <file>

The -f parameter will cause bcftools to overwrite an existing index file.

NOTE: Older versions of bcftools required the user to pass -m0 instead of -t for creating a tabix index.

Sorting CSV files before an import

You must have GNU coreutils installed in your system.

sort [-T <tmp_directory>] -t, -k2,2n -k1,1n -o <sorted_output.csv> <input.csv>

If you have a list of sorted CSV files and wish to merge them into a single sorted CSV file:

sort [-T <tmp_directory>] -m -t, -k2,2n -k1,1n -o <sorted_output.csv> <input_csv_list>