pairtools
Overview
Quickstart
Installation
Parsing sequence alignments into Hi-C pairs
Sorting pairs
Formats for storing Hi-C pairs
Pairtools stats
as a source of quality control metrics
Workflows and Parameters
Design notes
Command-line API
Tutorials
Pairtools walkthrough
Pairtools restrict walkthrough
Pairtools phase walkthrough
Pairtools benchmarking
pairtools
Index
Index
Symbols
|
C
|
F
|
I
|
P
|
S
Symbols
--add-columns
pairtools-parse command line option
pairtools-parse2 command line option
--add-pair-index
pairtools-parse command line option
pairtools-parse2 command line option
--assembly
pairtools-header-generate command line option
pairtools-parse command line option
pairtools-parse2 command line option
--backend
pairtools-dedup command line option
--bytile-dups
pairtools-stats command line option
--c1
pairtools-dedup command line option
pairtools-filterbycov command line option
pairtools-sort command line option
--c2
pairtools-dedup command line option
pairtools-filterbycov command line option
pairtools-sort command line option
--carryover
pairtools-dedup command line option
--chrom-subset
pairtools-dedup command line option
pairtools-select command line option
pairtools-stats command line option
--chroms-path
pairtools-flip command line option
pairtools-header-generate command line option
pairtools-parse command line option
pairtools-parse2 command line option
--chunksize
pairtools-dedup command line option
pairtools-scaling command line option
--clean-output
pairtools-phase command line option
--cmd-in
pairtools-dedup command line option
pairtools-filterbycov command line option
pairtools-flip command line option
pairtools-header-generate command line option
pairtools-header-set-columns command line option
pairtools-header-transfer command line option
pairtools-header-validate-columns command line option
pairtools-markasdup command line option
pairtools-merge command line option
pairtools-parse command line option
pairtools-parse2 command line option
pairtools-phase command line option
pairtools-restrict command line option
pairtools-sample command line option
pairtools-scaling command line option
pairtools-select command line option
pairtools-sort command line option
pairtools-split command line option
pairtools-stats command line option
--cmd-out
pairtools-dedup command line option
pairtools-filterbycov command line option
pairtools-flip command line option
pairtools-header-generate command line option
pairtools-header-set-columns command line option
pairtools-header-transfer command line option
pairtools-header-validate-columns command line option
pairtools-markasdup command line option
pairtools-merge command line option
pairtools-parse command line option
pairtools-parse2 command line option
pairtools-phase command line option
pairtools-restrict command line option
pairtools-sample command line option
pairtools-scaling command line option
pairtools-select command line option
pairtools-sort command line option
pairtools-split command line option
pairtools-stats command line option
--columns
pairtools-header-generate command line option
pairtools-header-set-columns command line option
--comment-char
pairtools-filterbycov command line option
--compress-program
pairtools-merge command line option
pairtools-sort command line option
--concatenate
pairtools-merge command line option
--debug
pairtools command line option
--dedup-max-mismatch
pairtools-parse2 command line option
--dist-range
pairtools-scaling command line option
--drop-readid
pairtools-parse command line option
pairtools-parse2 command line option
--drop-sam
pairtools-parse command line option
pairtools-parse2 command line option
--drop-seq
pairtools-parse command line option
pairtools-parse2 command line option
--engine
pairtools-dedup command line option
pairtools-stats command line option
--expand
pairtools-parse2 command line option
--extra-col
pairtools-sort command line option
--extra-col-pair
pairtools-dedup command line option
--extra-columns
pairtools-header-generate command line option
--filter
pairtools-dedup command line option
pairtools-stats command line option
--flip
pairtools-parse command line option
pairtools-parse2 command line option
--frags
pairtools-restrict command line option
--keep-first-header
pairtools-merge command line option
--keep-parent-id
pairtools-dedup command line option
--keep-readid
pairtools-parse2 command line option
--keep-sam
pairtools-parse2 command line option
--keep-seq
pairtools-parse2 command line option
--mark-dups
pairtools-dedup command line option
--mark-multi
pairtools-filterbycov command line option
--max-cov
pairtools-filterbycov command line option
--max-dist
pairtools-filterbycov command line option
--max-expansion-depth
pairtools-parse2 command line option
--max-insert-size
pairtools-parse2 command line option
--max-inter-align-gap
pairtools-parse command line option
pairtools-parse2 command line option
--max-mismatch
pairtools-dedup command line option
--max-molecule-size
pairtools-parse command line option
--max-nmerge
pairtools-merge command line option
--memory
pairtools-merge command line option
pairtools-sort command line option
--merge
pairtools-stats command line option
--method
pairtools-dedup command line option
pairtools-filterbycov command line option
--min-mapq
pairtools-parse command line option
pairtools-parse2 command line option
--n-dist-bins-decade
pairtools-scaling command line option
pairtools-stats command line option
--n-proc
pairtools-dedup command line option
--no-bytile-dups
pairtools-stats command line option
--no-chromsizes
pairtools-stats command line option
--no-concatenate
pairtools-merge command line option
--no-expand
pairtools-parse2 command line option
--no-flip
pairtools-header-generate command line option
pairtools-parse command line option
pairtools-parse2 command line option
--no-keep-first-header
pairtools-merge command line option
--no-mark-dups
pairtools-dedup command line option
--no-report-scores
pairtools-phase command line option
--no-yaml
pairtools-dedup command line option
pairtools-stats command line option
--nproc
pairtools-merge command line option
pairtools-sort command line option
--nproc-in
pairtools-dedup command line option
pairtools-filterbycov command line option
pairtools-flip command line option
pairtools-header-generate command line option
pairtools-header-set-columns command line option
pairtools-header-transfer command line option
pairtools-header-validate-columns command line option
pairtools-markasdup command line option
pairtools-merge command line option
pairtools-parse command line option
pairtools-parse2 command line option
pairtools-phase command line option
pairtools-restrict command line option
pairtools-sample command line option
pairtools-scaling command line option
pairtools-select command line option
pairtools-sort command line option
pairtools-split command line option
pairtools-stats command line option
--nproc-out
pairtools-dedup command line option
pairtools-filterbycov command line option
pairtools-flip command line option
pairtools-header-generate command line option
pairtools-header-set-columns command line option
pairtools-header-transfer command line option
pairtools-header-validate-columns command line option
pairtools-markasdup command line option
pairtools-merge command line option
pairtools-parse command line option
pairtools-parse2 command line option
pairtools-phase command line option
pairtools-restrict command line option
pairtools-sample command line option
pairtools-scaling command line option
pairtools-select command line option
pairtools-sort command line option
pairtools-split command line option
pairtools-stats command line option
--output
pairtools-dedup command line option
pairtools-filterbycov command line option
pairtools-flip command line option
pairtools-header-generate command line option
pairtools-header-set-columns command line option
pairtools-header-transfer command line option
pairtools-header-validate-columns command line option
pairtools-markasdup command line option
pairtools-merge command line option
pairtools-parse command line option
pairtools-parse2 command line option
pairtools-phase command line option
pairtools-restrict command line option
pairtools-sample command line option
pairtools-scaling command line option
pairtools-select command line option
pairtools-sort command line option
pairtools-stats command line option
--output-bytile-stats
pairtools-dedup command line option
pairtools-stats command line option
--output-dups
pairtools-dedup command line option
--output-highcov
pairtools-filterbycov command line option
--output-pairs
pairtools-split command line option
--output-parsed-alignments
pairtools-parse command line option
pairtools-parse2 command line option
--output-profile
pairtools command line option
--output-rest
pairtools-select command line option
--output-sam
pairtools-split command line option
--output-stats
pairtools-dedup command line option
pairtools-filterbycov command line option
pairtools-parse command line option
pairtools-parse2 command line option
--output-unmapped
pairtools-dedup command line option
pairtools-filterbycov command line option
--p1
pairtools-dedup command line option
pairtools-filterbycov command line option
pairtools-sort command line option
--p2
pairtools-dedup command line option
pairtools-filterbycov command line option
pairtools-sort command line option
--pairs
pairtools-header-generate command line option
--pairsam
pairtools-header-generate command line option
--phase-suffixes
pairtools-phase command line option
--post-mortem
pairtools command line option
--pt
pairtools-sort command line option
--readid-transform
pairtools-parse command line option
pairtools-parse2 command line option
--reference-columns
pairtools-header-validate-columns command line option
--reference-file
pairtools-header-transfer command line option
pairtools-header-validate-columns command line option
--regions
pairtools-scaling command line option
--remove-columns
pairtools-select command line option
--report-alignment-end
pairtools-parse command line option
--report-orientation
pairtools-parse2 command line option
--report-position
pairtools-parse2 command line option
--report-scores
pairtools-phase command line option
--s1
pairtools-dedup command line option
pairtools-filterbycov command line option
--s2
pairtools-dedup command line option
pairtools-filterbycov command line option
--sam-path
pairtools-header-generate command line option
--seed
pairtools-sample command line option
--send-header-to
pairtools-dedup command line option
pairtools-filterbycov command line option
--sep
pairtools-dedup command line option
pairtools-filterbycov command line option
--single-end
pairtools-parse2 command line option
--startup-code
pairtools-dedup command line option
pairtools-select command line option
pairtools-stats command line option
--tag-mode
pairtools-phase command line option
--tmpdir
pairtools-merge command line option
pairtools-sort command line option
--type-cast
pairtools-dedup command line option
pairtools-select command line option
pairtools-stats command line option
--unmapped-chrom
pairtools-dedup command line option
pairtools-filterbycov command line option
--verbose
pairtools command line option
--version
pairtools command line option
--view
pairtools-scaling command line option
--walks-policy
pairtools-parse command line option
--with-chromsizes
pairtools-stats command line option
--yaml
pairtools-dedup command line option
pairtools-stats command line option
-c
pairtools-flip command line option
pairtools-header-set-columns command line option
pairtools-header-validate-columns command line option
pairtools-parse command line option
pairtools-parse2 command line option
-d
pairtools command line option
-f
pairtools-restrict command line option
-o
pairtools-dedup command line option
pairtools-filterbycov command line option
pairtools-flip command line option
pairtools-header-generate command line option
pairtools-header-set-columns command line option
pairtools-header-transfer command line option
pairtools-header-validate-columns command line option
pairtools-markasdup command line option
pairtools-merge command line option
pairtools-parse command line option
pairtools-parse2 command line option
pairtools-phase command line option
pairtools-restrict command line option
pairtools-sample command line option
pairtools-scaling command line option
pairtools-select command line option
pairtools-sort command line option
pairtools-stats command line option
-p
pairtools-dedup command line option
-r
pairtools-header-transfer command line option
pairtools-header-validate-columns command line option
pairtools-select command line option
-s
pairtools-sample command line option
-t
pairtools-dedup command line option
pairtools-select command line option
pairtools-stats command line option
-v
pairtools command line option
C
CONDITION
pairtools-select command line option
F
FRACTION
pairtools-sample command line option
I
INPUT_PATH
pairtools-scaling command line option
pairtools-stats command line option
P
PAIRS_PATH
pairtools-dedup command line option
pairtools-filterbycov command line option
pairtools-flip command line option
pairtools-header-generate command line option
pairtools-header-set-columns command line option
pairtools-header-transfer command line option
pairtools-header-validate-columns command line option
pairtools-merge command line option
pairtools-phase command line option
pairtools-restrict command line option
pairtools-sample command line option
pairtools-select command line option
pairtools-sort command line option
PAIRSAM_PATH
pairtools-markasdup command line option
pairtools-split command line option
pairtools command line option
--debug
--output-profile
--post-mortem
--verbose
--version
-d
-v
pairtools-dedup command line option
--backend
--c1
--c2
--carryover
--chrom-subset
--chunksize
--cmd-in
--cmd-out
--engine
--extra-col-pair
--filter
--keep-parent-id
--mark-dups
--max-mismatch
--method
--n-proc
--no-mark-dups
--no-yaml
--nproc-in
--nproc-out
--output
--output-bytile-stats
--output-dups
--output-stats
--output-unmapped
--p1
--p2
--s1
--s2
--send-header-to
--sep
--startup-code
--type-cast
--unmapped-chrom
--yaml
-o
-p
-t
PAIRS_PATH
pairtools-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
PAIRS_PATH
pairtools-flip command line option
--chroms-path
--cmd-in
--cmd-out
--nproc-in
--nproc-out
--output
-c
-o
PAIRS_PATH
pairtools-header-generate command line option
--assembly
--chroms-path
--cmd-in
--cmd-out
--columns
--extra-columns
--no-flip
--nproc-in
--nproc-out
--output
--pairs
--pairsam
--sam-path
-o
PAIRS_PATH
pairtools-header-set-columns command line option
--cmd-in
--cmd-out
--columns
--nproc-in
--nproc-out
--output
-c
-o
PAIRS_PATH
pairtools-header-transfer command line option
--cmd-in
--cmd-out
--nproc-in
--nproc-out
--output
--reference-file
-o
-r
PAIRS_PATH
pairtools-header-validate-columns command line option
--cmd-in
--cmd-out
--nproc-in
--nproc-out
--output
--reference-columns
--reference-file
-c
-o
-r
PAIRS_PATH
pairtools-markasdup command line option
--cmd-in
--cmd-out
--nproc-in
--nproc-out
--output
-o
PAIRSAM_PATH
pairtools-merge command line option
--cmd-in
--cmd-out
--compress-program
--concatenate
--keep-first-header
--max-nmerge
--memory
--no-concatenate
--no-keep-first-header
--nproc
--nproc-in
--nproc-out
--output
--tmpdir
-o
PAIRS_PATH
pairtools-parse command line option
--add-columns
--add-pair-index
--assembly
--chroms-path
--cmd-in
--cmd-out
--drop-readid
--drop-sam
--drop-seq
--flip
--max-inter-align-gap
--max-molecule-size
--min-mapq
--no-flip
--nproc-in
--nproc-out
--output
--output-parsed-alignments
--output-stats
--readid-transform
--report-alignment-end
--walks-policy
-c
-o
SAM_PATH
pairtools-parse2 command line option
--add-columns
--add-pair-index
--assembly
--chroms-path
--cmd-in
--cmd-out
--dedup-max-mismatch
--drop-readid
--drop-sam
--drop-seq
--expand
--flip
--keep-readid
--keep-sam
--keep-seq
--max-expansion-depth
--max-insert-size
--max-inter-align-gap
--min-mapq
--no-expand
--no-flip
--nproc-in
--nproc-out
--output
--output-parsed-alignments
--output-stats
--readid-transform
--report-orientation
--report-position
--single-end
-c
-o
SAM_PATH
pairtools-phase command line option
--clean-output
--cmd-in
--cmd-out
--no-report-scores
--nproc-in
--nproc-out
--output
--phase-suffixes
--report-scores
--tag-mode
-o
PAIRS_PATH
pairtools-restrict command line option
--cmd-in
--cmd-out
--frags
--nproc-in
--nproc-out
--output
-f
-o
PAIRS_PATH
pairtools-sample command line option
--cmd-in
--cmd-out
--nproc-in
--nproc-out
--output
--seed
-o
-s
FRACTION
PAIRS_PATH
pairtools-scaling command line option
--chunksize
--cmd-in
--cmd-out
--dist-range
--n-dist-bins-decade
--nproc-in
--nproc-out
--output
--regions
--view
-o
INPUT_PATH
pairtools-select command line option
--chrom-subset
--cmd-in
--cmd-out
--nproc-in
--nproc-out
--output
--output-rest
--remove-columns
--startup-code
--type-cast
-o
-r
-t
CONDITION
PAIRS_PATH
pairtools-sort command line option
--c1
--c2
--cmd-in
--cmd-out
--compress-program
--extra-col
--memory
--nproc
--nproc-in
--nproc-out
--output
--p1
--p2
--pt
--tmpdir
-o
PAIRS_PATH
pairtools-split command line option
--cmd-in
--cmd-out
--nproc-in
--nproc-out
--output-pairs
--output-sam
PAIRSAM_PATH
pairtools-stats command line option
--bytile-dups
--chrom-subset
--cmd-in
--cmd-out
--engine
--filter
--merge
--n-dist-bins-decade
--no-bytile-dups
--no-chromsizes
--no-yaml
--nproc-in
--nproc-out
--output
--output-bytile-stats
--startup-code
--type-cast
--with-chromsizes
--yaml
-o
-t
INPUT_PATH
S
SAM_PATH
pairtools-parse command line option
pairtools-parse2 command line option