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Get candidate introgressed fragments

Input

To obtain candidate introgressed fragments from sstar, users should provide the output (e.g. test.tract.threshold) from sstar threshold. If no source genome is available, users can use the following command:

sstar tract --threshold test.tract.threshold --output-prefix test

If one source individual is available, users also can calculate source match rates and output these source match rates and candidate introgressed regions in a single BED file.

sstar tract --threshold test.tract.threshold --output-prefix test --match-rate test.tract.src1.match.rate

If source genomes from two different source populations are available, users could provide the output (e.g. test.tract.src1.match.rate and test.tract.src2.match.rate) from sstar matchrate, and use the following command:

sstar tract --threshold test.tract.threshold --output-prefix test --match-rate test.tract.src1.match.rate test.tract.src2.match.rate

Output

BED files containing candidate introgressed fragments will be generated, e.g. test.tract.exp.bed

An example for the output is below:
1 75030000 75080000 tsk_10 0.280797
  • The first column is the name of the chromosome.
  • The second column is the start position.
  • The third column is the end position.
  • The fourth column is the name of the sample.
  • The fifth column is the source match rate.