Index

Symbols

--cache-size tsinfer-match command line option tsinfer-run command line option --force tsinfer-augment-sites command line option tsinfer-infer-ancestors command line option tsinfer-match command line option tsinfer-post-process command line option tsinfer-run command line option --genotype-encoding tsinfer-infer-ancestors command line option tsinfer-run command line option --group-stop tsinfer-match command line option --input tsinfer-augment-sites command line option tsinfer-post-process command line option --keep-intermediates tsinfer-match command line option --log-file tsinfer-augment-sites command line option tsinfer-infer-ancestors command line option tsinfer-match command line option tsinfer-post-process command line option tsinfer-run command line option --match-file tsinfer-match command line option tsinfer-run command line option --output tsinfer-augment-sites command line option --progress tsinfer-augment-sites command line option tsinfer-infer-ancestors command line option tsinfer-match command line option tsinfer-post-process command line option tsinfer-run command line option --read-workers tsinfer-match command line option tsinfer-run command line option --threads tsinfer-augment-sites command line option tsinfer-infer-ancestors command line option tsinfer-match command line option tsinfer-post-process command line option tsinfer-run command line option --verbose tsinfer-augment-sites command line option tsinfer-infer-ancestors command line option tsinfer-match command line option tsinfer-post-process command line option tsinfer-run command line option

--version tsinfer command line option --workdir tsinfer-match command line option --write-threads tsinfer-infer-ancestors command line option -c tsinfer-match command line option tsinfer-run command line option -f tsinfer-augment-sites command line option tsinfer-infer-ancestors command line option tsinfer-match command line option tsinfer-post-process command line option tsinfer-run command line option -l tsinfer-augment-sites command line option tsinfer-infer-ancestors command line option tsinfer-match command line option tsinfer-post-process command line option tsinfer-run command line option -p tsinfer-augment-sites command line option tsinfer-infer-ancestors command line option tsinfer-match command line option tsinfer-post-process command line option tsinfer-run command line option -t tsinfer-augment-sites command line option tsinfer-infer-ancestors command line option tsinfer-match command line option tsinfer-post-process command line option tsinfer-run command line option -v tsinfer-augment-sites command line option tsinfer-infer-ancestors command line option tsinfer-match command line option tsinfer-post-process command line option tsinfer-run command line option -w tsinfer-infer-ancestors command line option

C

CONFIG tsinfer-augment-sites command line option tsinfer-config-check command line option tsinfer-config-show command line option tsinfer-infer-ancestors command line option tsinfer-match command line option tsinfer-post-process command line option tsinfer-run command line option

J

JSON_FILE tsinfer-show-match-jobs command line option

T

tsinfer command line option --version tsinfer-augment-sites command line option --force --input --log-file --output --progress --threads --verbose -f -l -p -t -v CONFIG tsinfer-config-check command line option CONFIG tsinfer-config-show command line option CONFIG tsinfer-infer-ancestors command line option --force --genotype-encoding --log-file --progress --threads --verbose --write-threads -f -l -p -t -v -w CONFIG tsinfer-match command line option --cache-size --force --group-stop --keep-intermediates --log-file --match-file --progress --read-workers --threads --verbose --workdir -c -f -l -p -t -v CONFIG

tsinfer-post-process command line option --force --input --log-file --progress --threads --verbose -f -l -p -t -v CONFIG tsinfer-run command line option --cache-size --force --genotype-encoding --log-file --match-file --progress --read-workers --threads --verbose -c -f -l -p -t -v CONFIG tsinfer-show-match-jobs command line option JSON_FILE