What do you need to know about bcftools commands?
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
How to set the prior mutation rate in snakemake?
A particularly important one is the prior mutation rate (1e-3 per default). It is set via the flag -P of the bcftools call command. Consider making this flag configurable via adding a new key to the config file and using the params directive in the rule bcftools_call to propagate it to the shell command.
What happens to the output file in snakemake?
After successful execution of the job, Snakemake will write-protect the output file in the filesystem, so that it can’t be overwritten or deleted by accident. Re-execute the whole workflow and observe how Snakemake handles the temporary and protected files.
When to use multiple threads in snakemake example?
Snakemake can be made aware of the threads a rule needs with the threads directive. In our example workflow, it makes sense to use multiple threads for the rule bwa_map:
How to filter a file with bcftools query?
$ bcftools query -e’GT =”.”‘ -f’%CHROM %POS [ %GT] ‘ file.bcf | head -2 1 69511 1/1 1/1 1 71850 0/0 0/1 Say our VCF contains the per-sample depth and genotype quality annotations and we want to include only sites where one or more samples have big enough coverage ( DP>10) and genotype quality ( GQ>20 ).
How to skip sites in bcftools-GitHub page?
Skip sites where FILTER column does not contain any of the strings listed in LIST. For example, to include only sites which have no filters set, use -f .,PASS . Do not append version and command line information to the output VCF header.
What kind of stream does bcftools work on?
BCFtools is designed to work on a stream. It regards an input file “-” as the standard input (stdin) and outputs to the standard output (stdout). Several commands can thus be combined with Unix pipes. The BCF1 format output by versions of samtools <= 0.1.19 is not compatible with this version of bcftools.