Index

Symbols

--add-columns pairsamtools-parse command line option --assembly pairsamtools-parse command line option --c1 pairsamtools-dedup command line option pairsamtools-filterbycov command line option --c2 pairsamtools-dedup command line option pairsamtools-filterbycov command line option --chrom-subset pairsamtools-select command line option --chroms-path pairsamtools-parse command line option --clean-output pairsamtools-phase command line option --cmd-in pairsamtools-dedup command line option pairsamtools-filterbycov command line option pairsamtools-markasdup command line option pairsamtools-merge command line option pairsamtools-parse command line option pairsamtools-phase command line option pairsamtools-restrict command line option pairsamtools-select command line option pairsamtools-sort command line option pairsamtools-split command line option pairsamtools-stats command line option --cmd-out pairsamtools-dedup command line option pairsamtools-filterbycov command line option pairsamtools-markasdup command line option pairsamtools-merge command line option pairsamtools-parse command line option pairsamtools-phase command line option pairsamtools-restrict command line option pairsamtools-select command line option pairsamtools-sort command line option pairsamtools-split command line option pairsamtools-stats command line option --comment-char pairsamtools-dedup command line option pairsamtools-filterbycov command line option --compress-program pairsamtools-merge command line option pairsamtools-sort command line option --drop-readid pairsamtools-parse command line option --drop-sam pairsamtools-parse command line option --drop-seq pairsamtools-parse command line option --extra-col-pair pairsamtools-dedup command line option --frags pairsamtools-restrict command line option --mark-dups pairsamtools-dedup command line option --mark-multi pairsamtools-filterbycov command line option --max-cov pairsamtools-filterbycov command line option --max-dist pairsamtools-filterbycov command line option --max-inter-align-gap pairsamtools-parse command line option --max-mismatch pairsamtools-dedup command line option --max-molecule-size pairsamtools-parse command line option --max-nmerge pairsamtools-merge command line option --memory pairsamtools-merge command line option pairsamtools-sort command line option --merge pairsamtools-stats command line option --method pairsamtools-dedup command line option pairsamtools-filterbycov command line option --min-mapq pairsamtools-parse command line option --no-flip pairsamtools-parse command line option --nproc pairsamtools-merge command line option pairsamtools-sort command line option --nproc-in pairsamtools-dedup command line option pairsamtools-filterbycov command line option pairsamtools-markasdup command line option pairsamtools-merge command line option pairsamtools-parse command line option pairsamtools-phase command line option pairsamtools-restrict command line option pairsamtools-select command line option pairsamtools-sort command line option pairsamtools-split command line option pairsamtools-stats command line option

--nproc-out pairsamtools-dedup command line option pairsamtools-filterbycov command line option pairsamtools-markasdup command line option pairsamtools-merge command line option pairsamtools-parse command line option pairsamtools-phase command line option pairsamtools-restrict command line option pairsamtools-select command line option pairsamtools-sort command line option pairsamtools-split command line option pairsamtools-stats command line option --output pairsamtools-dedup command line option pairsamtools-filterbycov command line option pairsamtools-markasdup command line option pairsamtools-merge command line option pairsamtools-parse command line option pairsamtools-phase command line option pairsamtools-restrict command line option pairsamtools-select command line option pairsamtools-sort command line option pairsamtools-stats command line option --output-dups pairsamtools-dedup command line option --output-highcov pairsamtools-filterbycov command line option --output-pairs pairsamtools-split command line option --output-parsed-alignments pairsamtools-parse command line option --output-profile pairsamtools command line option --output-rest pairsamtools-select command line option --output-sam pairsamtools-split command line option --output-stats pairsamtools-dedup command line option pairsamtools-filterbycov command line option pairsamtools-parse command line option --output-unmapped pairsamtools-dedup command line option pairsamtools-filterbycov command line option --p1 pairsamtools-dedup command line option pairsamtools-filterbycov command line option --p2 pairsamtools-dedup command line option pairsamtools-filterbycov command line option --phase-suffixes pairsamtools-phase command line option --post-mortem pairsamtools command line option --report-alignment-end pairsamtools-parse command line option --s1 pairsamtools-dedup command line option pairsamtools-filterbycov command line option --s2 pairsamtools-dedup command line option pairsamtools-filterbycov command line option --send-comments-to pairsamtools-select command line option --send-header-to pairsamtools-dedup command line option pairsamtools-filterbycov command line option --sep pairsamtools-dedup command line option pairsamtools-filterbycov command line option --tmpdir pairsamtools-merge command line option pairsamtools-sort command line option --unmapped-chrom pairsamtools-dedup command line option pairsamtools-filterbycov command line option --version pairsamtools command line option --walks-policy pairsamtools-parse command line option -c pairsamtools-parse command line option -f pairsamtools-restrict command line option -o pairsamtools-dedup command line option pairsamtools-filterbycov command line option pairsamtools-markasdup command line option pairsamtools-merge command line option pairsamtools-parse command line option pairsamtools-phase command line option pairsamtools-restrict command line option pairsamtools-select command line option pairsamtools-sort command line option pairsamtools-stats command line option

C

CONDITION pairsamtools-select command line option

I

INPUT_PATH pairsamtools-stats command line option

P

PAIRSAM_PATH pairsamtools-dedup command line option pairsamtools-filterbycov command line option pairsamtools-markasdup command line option pairsamtools-merge command line option pairsamtools-phase command line option pairsamtools-restrict command line option pairsamtools-select command line option pairsamtools-sort command line option pairsamtools-split command line option pairsamtools command line option --output-profile --post-mortem --version pairsamtools-dedup command line option --c1 --c2 --cmd-in --cmd-out --comment-char --extra-col-pair --mark-dups --max-mismatch --method --nproc-in --nproc-out --output --output-dups --output-stats --output-unmapped --p1 --p2 --s1 --s2 --send-header-to --sep --unmapped-chrom -o PAIRSAM_PATH pairsamtools-filterbycov command line option --c1 --c2 --cmd-in --cmd-out --comment-char --mark-multi --max-cov --max-dist --method --nproc-in --nproc-out --output --output-highcov --output-stats --output-unmapped --p1 --p2 --s1 --s2 --send-header-to --sep --unmapped-chrom -o PAIRSAM_PATH pairsamtools-markasdup command line option --cmd-in --cmd-out --nproc-in --nproc-out --output -o PAIRSAM_PATH pairsamtools-merge command line option --cmd-in --cmd-out --compress-program --max-nmerge --memory --nproc --nproc-in --nproc-out --output --tmpdir -o PAIRSAM_PATH

pairsamtools-parse command line option --add-columns --assembly --chroms-path --cmd-in --cmd-out --drop-readid --drop-sam --drop-seq --max-inter-align-gap --max-molecule-size --min-mapq --no-flip --nproc-in --nproc-out --output --output-parsed-alignments --output-stats --report-alignment-end --walks-policy -c -o SAM_PATH pairsamtools-phase command line option --clean-output --cmd-in --cmd-out --nproc-in --nproc-out --output --phase-suffixes -o PAIRSAM_PATH pairsamtools-restrict command line option --cmd-in --cmd-out --frags --nproc-in --nproc-out --output -f -o PAIRSAM_PATH pairsamtools-select command line option --chrom-subset --cmd-in --cmd-out --nproc-in --nproc-out --output --output-rest --send-comments-to -o CONDITION PAIRSAM_PATH pairsamtools-sort command line option --cmd-in --cmd-out --compress-program --memory --nproc --nproc-in --nproc-out --output --tmpdir -o PAIRSAM_PATH pairsamtools-split command line option --cmd-in --cmd-out --nproc-in --nproc-out --output-pairs --output-sam PAIRSAM_PATH pairsamtools-stats command line option --cmd-in --cmd-out --merge --nproc-in --nproc-out --output -o INPUT_PATH

S

SAM_PATH pairsamtools-parse command line option