360607541994aa88b49fc241c34bd964a1db7b50 lrnassar Tue Sep 29 15:07:07 2026 -0700 Rebuild the hs1 sgdpCopyNumber track as a faceted composite, so its 319 samples are picked from a searchable metadata table rather than 319 checkboxes; the same bigBeds are pointed at by the same /gbdb paths, so no data changed. Subtracks are renamed from ___wssd to sgdpCopyNumber_ because a faceted composite requires the parent name plus the primaryKey value, and dataTypes is deliberately unset: with it hgTrackUi parses the data element only as far as the first underscore and would truncate LP6005441-DNA_A01 to LP6005441-DNA. The per-subtrack 'visibility dense' lines are gone because a faceted composite honors a child's own display mode where a classic composite ignores it, so keeping them would pin every sample to dense and remove the per-item click that the copy number is read from. Sample attributes come from the Reich lab SGDP tables and 317 of the 319 join; sgdpCopyNumberBuild.py takes its sample list from the checked-in sgdpCopyNumberSamples.tsv rather than from trackDb, because at release the generated stanzas replace sgdpCopyNumber.trackDb.ra and the legacy region prefix that the two unmatched samples depend on disappears with them. Alpha gets the new file and beta/public keep the old one until the metadata and color files are on the RR, without which the picker renders empty. sgdpCopyNumber_subset, which turns out to be the first 29 samples in plate order rather than any curated set, is not in the alpha version; whether it is retired for good is still open on the ticket. Faceted composite suggested by Gerardo, and the cross-sandbox metadata fetch that this track turned up was fixed by Max in b3a26a6aff3. refs #29344 diff --git src/hg/makeDb/trackDb/human/hs1/html/sgdpCopyNumber.html src/hg/makeDb/trackDb/human/hs1/html/sgdpCopyNumber.html index 49d96f39653..4573af2ff14 100644 --- src/hg/makeDb/trackDb/human/hs1/html/sgdpCopyNumber.html +++ src/hg/makeDb/trackDb/human/hs1/html/sgdpCopyNumber.html @@ -1,380 +1,200 @@ +

Description

+

+Large parts of the human genome are present in more than the two copies a diploid genome would +otherwise carry, and the number of copies varies between people. Much of this variation falls in +segmental duplications, where it can change the dosage of the genes inside them. +

+

+This track shows copy number estimated along the genome for 317 individuals from the +Simons Genome Diversity Project (SGDP), a panel of high coverage genomes +sampled from more than 140 populations worldwide. Two further rows give the copy number of the +CHM13 and GRCh38 reference assemblies themselves, which are useful as a baseline when reading the +sample rows. Copy number is estimated in windows that each hold 500 bp of uniquely mappable +sequence, and each window is colored by the number of copies inferred there. Unmappable bases are +skipped, so a window covers more of the genome than 500 bp, typically around 1.7 kb. +

- -

Description

This track represents copy number estimates form -the -Simons Genome Diversity Project. Copy number is estimated over 500 bp -windows of uniquely mappable sequence. Sequences are colored from cold to hot -(0 - 120+) and exact copy can be found by clicking on the region of interest. - - +

Display Conventions and Configuration

+

+Each sample is a separate row. Because there are more than 300 of them, samples are chosen from a +searchable table on the track configuration page rather than from a list of checkboxes. The panel +to the left of that table filters the samples by geographic region, country, sex and DNA source, +and the search boxes above each column match on population, sample identifier and town. Pick the +rows you want and press Submit, and those samples appear in the browser in the order shown in the +table. +

+

+When the track is first turned on it shows the two reference rows and one sample from each of the +seven SGDP regions. The Minimum copy number filter, above the table, hides windows below +a copy number you choose, across every sample at once. +

+

+Set the track to pack, squish or full to read individual windows. Clicking a window opens a page +giving its exact copy number, which is a fractional value rather than the rounded number the color +represents. In dense mode the rows are merged and individual windows cannot be clicked. +

+

+Over centromeres and other satellite arrays almost nothing maps uniquely, so a single window can +stretch across tens of megabases and one value is drawn across the whole block. Those wide blocks +represent far less evidence per base than the narrow windows elsewhere. +

-

Code Availability

-GitHub +

Copy number color key

+ + + + + + + + + + + + + + + + + + + + + + + +
 0 copies
 1 copy
 2 copies, the usual diploid state
 3 copies
 4 copies
 5 copies
 6 copies
 7 copies
 8 copies
 9 copies
 10 to 19 copies
 20 to 29 copies
 30 to 39 copies
 40 to 49 copies
 50 to 59 copies
 60 to 69 copies
 70 to 79 copies
 80 to 89 copies
 90 to 99 copies
 100 to 109 copies
 110 to 119 copies
 120 copies or more
-

Copy Number Key

-
Copy numberColor
0
■
1
■
2
■
3
■
4
■
5
■
6
■
7
■
8
■
9
■
10
■
20
■
30
■
40
■
50
■
60
■
70
■
80
■
90
■
100
■
110
■
120
■
+

Methods

+

+Copy number was estimated from short read sequencing depth. Reads from each SGDP genome were +mapped to the T2T-CHM13v2.0 assembly, depth was counted in 500 bp windows of sequence that can be +mapped uniquely, corrected for GC content, and converted to a copy number by scaling against +regions of the genome taken to be present in two copies. This is the read depth approach of +Sudmant and colleagues, implemented in the +fastCN-smk pipeline. Each +estimate is a fractional value; the color in the display is that value rounded to a whole number +of copies. Every base of the assembly falls inside some window, so there are no gaps in the +display, but the windows are far from even in width. +

+

+The copy number files were produced by the T2T Consortium and downloaded from the Eichler lab at +eichlerlab.gs.washington.edu. The sample attributes shown in the +configuration table (region, country, population, sex, DNA source, coordinates and BioSample +accession) were taken from the SGDP sample tables published by the Reich lab at +sharehost.hms.harvard.edu and joined to the data files by sequencing library +identifier. Two samples are present in the data but not in the published sample tables. One of +them keeps the region and population its original track name carried, and the other has neither; +for both, every remaining column is left blank rather than filled in from another source. The +steps are recorded in our +makeDoc, and the scripts are in +our source tree. +

-

Data Access

+

Data Access

-The raw data can be explored interactively with the +The data can be explored interactively in table format with the Table Browser or the -Data Integrator. The data can also be -accessed from scripts through our REST -API.

+Data Integrator and exported from there to +spreadsheet or tab-separated tables. From scripts, the data can be accessed through our +API, track=sgdpCopyNumber. +

-This track is a container of multiple subtracks; the underlying data are stored in bigBed files -that can be downloaded from our -download server. -Individual regions or the whole genome annotation can be obtained using our tool +For automated download and analysis, each sample is stored in its own bigBed file that can be +downloaded from +our download +server. The files are named after the sequencing library, for example +LP6005441-DNA_A01_wssd.bb, and the configuration table gives the library identifier for +every sample. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found -here. -The tool can also be used to obtain only features within a given range, for example:

-bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/sgdpCopyNumber/LP6005441-DNA_A01_wssd.bb -chrom=chr6 -start=0 -end=1000000 stdout +here. The tool can also be used to obtain features within a given range, for +example: +

+

+bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/sgdpCopyNumber/LP6005441-DNA_A01_wssd.bb +-chrom=chr6 -start=0 -end=1000000 stdout +

Please refer to our mailing list archives for questions, or our Data Access FAQ for more -information.

+information. +

-

Credits

-Please feel free to contact William Harvey or Mitchell Vollger with any questions and/or concerns regarding this track. +

Credits

+

+Thanks to William Harvey and Mitchell Vollger of the Eichler lab, University of Washington, for +producing these data and making them available, and to the Simons Genome Diversity Project for the +underlying genomes. Please contact +William Harvey or +Mitchell Vollger with questions about the copy number +estimates themselves. +

+ +

References

-

References

-Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE. Recent segmental duplications in the human genome. Science 2002 -

-Pendleton AL, Shen F, Taravella AM, Emery S, Veeramah KR, Boyko AR, Kidd JM. Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication. BMC Biol. 2018 -

+

+Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, +Tandon A et al. + +The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. +Nature. 2016 Oct 13;538(7624):201-206. +PMID: 27654912; PMC: PMC5161557 +

-Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, et al. Global diversity, population stratification, and selection of human copy-number variation. Science. 2015 -

-Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, et al. Diversity of human copy number. Science. 2010 -

Sample table

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
SampleRead file
LP6005441-DNA_A01/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A01.srt.aln.bam
LP6005441-DNA_A03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A03.srt.aln.bam
LP6005441-DNA_A04/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A04.srt.aln.bam
LP6005441-DNA_A05/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A05.srt.aln.bam
LP6005441-DNA_A06/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A06.srt.aln.bam
LP6005441-DNA_A08/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A08.srt.aln.bam
LP6005441-DNA_A09/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A09.srt.aln.bam
LP6005441-DNA_A10/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A10.srt.aln.bam
LP6005441-DNA_A11/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A11.srt.aln.bam
LP6005441-DNA_A12/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_A12.srt.aln.bam
LP6005441-DNA_B01/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B01.srt.aln.bam
LP6005441-DNA_B02/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B02.srt.aln.bam
LP6005441-DNA_B03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B03.srt.aln.bam
LP6005441-DNA_B04/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B04.srt.aln.bam
LP6005441-DNA_B05/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B05.srt.aln.bam
LP6005441-DNA_B06/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B06.srt.aln.bam
LP6005441-DNA_B07/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B07.srt.aln.bam
LP6005441-DNA_B08/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B08.srt.aln.bam
LP6005441-DNA_B09/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B09.srt.aln.bam
LP6005441-DNA_B10/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B10.srt.aln.bam
LP6005441-DNA_B11/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B11.srt.aln.bam
LP6005441-DNA_B12/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_B12.srt.aln.bam
LP6005441-DNA_C02/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C02.srt.aln.bam
LP6005441-DNA_C03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C03.srt.aln.bam
LP6005441-DNA_C05/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C05.srt.aln.bam
LP6005441-DNA_C06/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C06.srt.aln.bam
LP6005441-DNA_C07/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C07.srt.aln.bam
LP6005441-DNA_C08/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C08.srt.aln.bam
LP6005441-DNA_C09/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C09.srt.aln.bam
LP6005441-DNA_C10/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C10.srt.aln.bam
LP6005441-DNA_C11/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_C11.srt.aln.bam
LP6005441-DNA_D01/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D01.srt.aln.bam
LP6005441-DNA_D02/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D02.srt.aln.bam
LP6005441-DNA_D03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D03.srt.aln.bam
LP6005441-DNA_D04/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D04.srt.aln.bam
LP6005441-DNA_D05/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D05.srt.aln.bam
LP6005441-DNA_D06/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D06.srt.aln.bam
LP6005441-DNA_D07/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D07.srt.aln.bam
LP6005441-DNA_D08/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D08.srt.aln.bam
LP6005441-DNA_D09/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D09.srt.aln.bam
LP6005441-DNA_D10/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D10.srt.aln.bam
LP6005441-DNA_D11/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D11.srt.aln.bam
LP6005441-DNA_D12/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_D12.srt.aln.bam
LP6005441-DNA_E02/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E02.srt.aln.bam
LP6005441-DNA_E03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E03.srt.aln.bam
LP6005441-DNA_E05/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E05.srt.aln.bam
LP6005441-DNA_E06/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E06.srt.aln.bam
LP6005441-DNA_E07/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E07.srt.aln.bam
LP6005441-DNA_E08/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E08.srt.aln.bam
LP6005441-DNA_E09/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E09.srt.aln.bam
LP6005441-DNA_E10/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_E10.srt.aln.bam
LP6005441-DNA_F01/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F01.srt.aln.bam
LP6005441-DNA_F02/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F02.srt.aln.bam
LP6005441-DNA_F03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F03.srt.aln.bam
LP6005441-DNA_F04/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F04.srt.aln.bam
LP6005441-DNA_F05/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F05.srt.aln.bam
LP6005441-DNA_F06/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F06.srt.aln.bam
LP6005441-DNA_F07/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F07.srt.aln.bam
LP6005441-DNA_F08/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F08.srt.aln.bam
LP6005441-DNA_F09/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F09.srt.aln.bam
LP6005441-DNA_F10/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F10.srt.aln.bam
LP6005441-DNA_F12/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_F12.srt.aln.bam
LP6005441-DNA_G02/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G02.srt.aln.bam
LP6005441-DNA_G03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G03.srt.aln.bam
LP6005441-DNA_G04/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G04.srt.aln.bam
LP6005441-DNA_G05/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G05.srt.aln.bam
LP6005441-DNA_G06/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G06.srt.aln.bam
LP6005441-DNA_G07/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G07.srt.aln.bam
LP6005441-DNA_G08/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G08.srt.aln.bam
LP6005441-DNA_G09/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G09.srt.aln.bam
LP6005441-DNA_G10/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G10.srt.aln.bam
LP6005441-DNA_G11/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G11.srt.aln.bam
LP6005441-DNA_G12/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_G12.srt.aln.bam
LP6005441-DNA_H02/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H02.srt.aln.bam
LP6005441-DNA_H03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H03.srt.aln.bam
LP6005441-DNA_H05/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H05.srt.aln.bam
LP6005441-DNA_H06/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H06.srt.aln.bam
LP6005441-DNA_H07/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H07.srt.aln.bam
LP6005441-DNA_H08/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H08.srt.aln.bam
LP6005441-DNA_H09/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H09.srt.aln.bam
LP6005441-DNA_H10/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H10.srt.aln.bam
LP6005441-DNA_H11/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H11.srt.aln.bam
LP6005441-DNA_H12/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005441-DNA_H12.srt.aln.bam
LP6005442-DNA_A02/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A02.srt.aln.bam
LP6005442-DNA_A03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A03.srt.aln.bam
LP6005442-DNA_A04/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A04.srt.aln.bam
LP6005442-DNA_A08/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A08.srt.aln.bam
LP6005442-DNA_A09/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A09.srt.aln.bam
LP6005442-DNA_A10/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A10.srt.aln.bam
LP6005442-DNA_A11/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A11.srt.aln.bam
LP6005442-DNA_A12/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_A12.srt.aln.bam
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LP6005442-DNA_B02/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005442-DNA_B02.srt.aln.bam
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LP6005519-DNA_H10/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005519-DNA_H10.srt.aln.bam
LP6005519-DNA_H12/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005519-DNA_H12.srt.aln.bam
LP6005592-DNA_A02/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005592-DNA_A02.srt.aln.bam
LP6005592-DNA_A04/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005592-DNA_A04.srt.aln.bam
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LP6005592-DNA_H03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005592-DNA_H03.srt.aln.bam
LP6005619-DNA_A01/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005619-DNA_A01.srt.aln.bam
LP6005619-DNA_B01/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005619-DNA_B01.srt.aln.bam
LP6005619-DNA_C01/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005619-DNA_C01.srt.aln.bam
LP6005619-DNA_D01/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005619-DNA_D01.srt.aln.bam
LP6005677-DNA_A02/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_A02.srt.aln.bam
LP6005677-DNA_A03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_A03.srt.aln.bam
LP6005677-DNA_A04/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_A04.srt.aln.bam
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LP6005677-DNA_B04/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_B04.srt.aln.bam
LP6005677-DNA_C03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_C03.srt.aln.bam
LP6005677-DNA_C04/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_C04.srt.aln.bam
LP6005677-DNA_D01/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_D01.srt.aln.bam
LP6005677-DNA_D03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_D03.srt.aln.bam
LP6005677-DNA_D04/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_D04.srt.aln.bam
LP6005677-DNA_E01/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_E01.srt.aln.bam
LP6005677-DNA_E03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_E03.srt.aln.bam
LP6005677-DNA_E04/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_E04.srt.aln.bam
LP6005677-DNA_F01/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_F01.srt.aln.bam
LP6005677-DNA_F03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_F03.srt.aln.bam
LP6005677-DNA_G01/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_G01.srt.aln.bam
LP6005677-DNA_G03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_G03.srt.aln.bam
LP6005677-DNA_H03/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6005677-DNA_H03.srt.aln.bam
LP6007068-DNA_A01/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6007068-DNA_A01.srt.aln.bam
LP6007069-DNA_A01/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/LP6007069-DNA_A01.srt.aln.bam
SS6004471/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/SS6004471.srt.aln.bam
SS6004477/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/SS6004477.srt.aln.bam
SS6004478/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/SS6004478.srt.aln.bam
SS6004480/net/eichler/vol28/projects/short_read_cohorts/nobackups/SGDP/SS6004480.srt.aln.bam
CHM13_kmer/net/eichler/vol27/projects/hprc/nobackups/analysis/kmer_fastcn/input/kmer/CHM13_v2.0/CHM13_v2.0.fa.gz
GRCh38_kmer/net/eichler/vol27/projects/hprc/nobackups/analysis/kmer_fastcn/input/kmer/GRCh38/GRCh38.fa.gz
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