unusual output from LD pruning
329 views
Skip to first unread message
Kaustubh Adhikari
Jun 27, 2014, 11:56:03 AM6/27/14
to plink2...@googlegroups.com
Running --indep on several datasets with Plink 1.9, I get odd values of the number of SNPs in a chromosome, e.g. "Pruned 60901 variants from chromosome 1, leaving 18446744073709550202."
Also, the number of SNPs removed, as reported, is greater than the actual number of SNPs in the file: "Pruning complete. 749770 of 730525 variants removed." In reality, 658084 markers were removed, as listed in plink.prune.out.
Two log files are attached below. The same output is seen with the 27 June development build. The log file from Plink 1.07 is also attached for the same command.
------------------------------------------------------------------------------------------------------------------------------------------
PLINK v1.90b2p 64-bit (17 Jun 2014)
6 arguments: --bfile r-temp --indep 50 5 2
Hostname: ANDRES-PC8064
Working directory: D:\Sequence data\ref12-nam4\PLINK
Start time: Fri Jun 27 15:10:45 2014
Random number seed: 1403878245
32693 MB RAM detected; reserving 16346 MB for main workspace.
730525 variants loaded from .bim file.
8 people (0 males, 0 females, 8 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
Using 1 thread (no multithreaded calculations invoked).
Calculating allele frequencies... done.
Warning: Nonmissing nonmale Y chromosome genotype(s) present.
Total genotyping rate is 0.812604.
730525 variants and 8 people pass filters and QC.
Note: No phenotypes present.
Pruned 60901 variants from chromosome 1, leaving 18446744073709550202.
Pruned 59699 variants from chromosome 2, leaving 18446744073709549866.
Pruned 48744 variants from chromosome 3, leaving 18446744073709550302.
Pruned 41958 variants from chromosome 4, leaving 18446744073709550264.
Pruned 43460 variants from chromosome 5, leaving 18446744073709550428.
Pruned 49470 variants from chromosome 6, leaving 18446744073709550656.
Pruned 39690 variants from chromosome 7, leaving 18446744073709550243.
Pruned 38052 variants from chromosome 8, leaving 18446744073709550766.
Pruned 34054 variants from chromosome 9, leaving 18446744073709550536.
Pruned 40531 variants from chromosome 10, leaving 18446744073709550343.
Pruned 37716 variants from chromosome 11, leaving 18446744073709550731.
Pruned 36778 variants from chromosome 12, leaving 18446744073709550560.
Pruned 28808 variants from chromosome 13, leaving 18446744073709550771.
Pruned 24071 variants from chromosome 14, leaving 18446744073709550981.
Pruned 22605 variants from chromosome 15, leaving 18446744073709550787.
Pruned 23628 variants from chromosome 16, leaving 18446744073709550881.
Pruned 21081 variants from chromosome 17, leaving 18446744073709550907.
Pruned 22626 variants from chromosome 18, leaving 18446744073709550790.
Pruned 15754 variants from chromosome 19, leaving 18446744073709551073.
Pruned 18859 variants from chromosome 20, leaving 18446744073709551283.
Pruned 10590 variants from chromosome 21, leaving 18446744073709551318.
Pruned 10923 variants from chromosome 22, leaving 18446744073709551224.
Pruned 17896 variants from chromosome 23, leaving 159.
Pruned 1409 variants from chromosome 24, leaving 0.
Pruned 467 variants from chromosome 25, leaving 6.
Pruning complete. 749770 of 730525 variants removed.
Marker lists written to plink.prune.in and plink.prune.out .
End time: Fri Jun 27 15:10:54 2014
------------------------------------------------------------------------------------------------------------------------------------------
PLINK v1.90b2p 64-bit (17 Jun 2014)
6 arguments: --bfile r-temp --indep 50 5 2
Hostname: ANDRES-PC8064
Working directory: D:\Sequence data\ref12-nam4\PLINK
Start time: Fri Jun 27 15:14:56 2014
Random number seed: 1403878496
32693 MB RAM detected; reserving 16346 MB for main workspace.
730525 variants loaded from .bim file.
8 people (0 males, 0 females, 8 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
Using 1 thread (no multithreaded calculations invoked).
Calculating allele frequencies... done.
Warning: Nonmissing nonmale Y chromosome genotype(s) present.
Total genotyping rate is 0.819564.
730525 variants and 8 people pass filters and QC.
Note: No phenotypes present.
Pruned 59034 variants from chromosome 1, leaving 453.
Pruned 57387 variants from chromosome 2, leaving 562.
Pruned 46899 variants from chromosome 3, leaving 531.
Pruned 40294 variants from chromosome 4, leaving 312.
Pruned 41933 variants from chromosome 5, leaving 339.
Pruned 48088 variants from chromosome 6, leaving 422.
Pruned 38168 variants from chromosome 7, leaving 149.
Pruned 37015 variants from chromosome 8, leaving 187.
Pruned 32843 variants from chromosome 9, leaving 131.
Pruned 39001 variants from chromosome 10, leaving 257.
Pruned 36537 variants from chromosome 11, leaving 294.
Pruned 35607 variants from chromosome 12, leaving 115.
Pruned 27945 variants from chromosome 13, leaving 18.
Pruned 23253 variants from chromosome 14, leaving 183.
Pruned 21718 variants from chromosome 15, leaving 58.
Pruned 22779 variants from chromosome 16, leaving 114.
Pruned 20305 variants from chromosome 17, leaving 67.
Pruned 21668 variants from chromosome 18, leaving 132.
Pruned 15103 variants from chromosome 19, leaving 108.
Pruned 18309 variants from chromosome 20, leaving 217.
Pruned 10202 variants from chromosome 21, leaving 90.
Pruned 10537 variants from chromosome 22, leaving 18446744073709551610.
Pruned 17668 variants from chromosome 23, leaving 387.
Pruned 1409 variants from chromosome 24, leaving 0.
Pruned 483 variants from chromosome 25, leaving 18446744073709551606.
Pruning complete. 724185 of 730525 variants removed.
Marker lists written to plink.prune.in and plink.prune.out .
End time: Fri Jun 27 15:15:01 2014
------------------------------------------------------------------------------------------------------------------------------------------
@----------------------------------------------------------@
| PLINK! | v1.07 | 10/Aug/2009 |
|----------------------------------------------------------|
| (C) 2009 Shaun Purcell, GNU General Public License, v2 |
|----------------------------------------------------------|
| For documentation, citation & bug-report instructions: |
| http://pngu.mgh.harvard.edu/purcell/plink/ |
@----------------------------------------------------------@
Web-based version check ( --noweb to skip )
Recent cached web-check found... OK, v1.07 is current
+++ PLINK 1.9 is now available! See above website for details +++
Writing this text to log file [ plink.log ]
Analysis started: Fri Jun 27 15:44:01 2014
Options in effect:
--bfile r-temp
--indep 50 5 2
Reading map (extended format) from [ r-temp.bim ]
730525 markers to be included from [ r-temp.bim ]
Reading pedigree information from [ r-temp.fam ]
8 individuals read from [ r-temp.fam ]
0 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 0 controls and 8 missing
0 males, 0 females, and 8 of unspecified sex
Warning, found 8 individuals with ambiguous sex codes
These individuals will be set to missing ( or use --allow-no-sex )
Writing list of these individuals to [ plink.nosex ]
Reading genotype bitfile from [ r-temp.bed ]
Detected that binary PED file is v1.00 SNP-major mode
Before frequency and genotyping pruning, there are 730525 SNPs
8 founders and 0 non-founders found
707 SNPs with no founder genotypes observed
Warning, MAF set to 0 for these SNPs (see --nonfounders)
Writing list of these SNPs to [ plink.nof ]
Total genotyping rate in remaining individuals is nan
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 730525 SNPs
After filtering, 0 cases, 0 controls and 8 missing
After filtering, 0 males, 0 females, and 8 of unspecified sex
Performing LD-based pruning...
Writing pruned-in SNPs to [ plink.prune.in ]
Writing pruned-out SNPs to [ plink.prune.out ]
Scanning from chromosome 0 to XY
Skippng chromosome 0
Scan region on chromosome 1 from [ rs4477212 ] to [ rs12746903 ]
For chromosome 1, 50864 SNPs pruned out, 8623 remaining
Scan region on chromosome 2 from [ rs10195681 ] to [ rs12478296 ]
For chromosome 2, 49763 SNPs pruned out, 8186 remaining
Scan region on chromosome 3 from [ rs13060385 ] to [ rs10433653 ]
For chromosome 3, 40636 SNPs pruned out, 6794 remaining
Scan region on chromosome 4 from [ rs13125929 ] to [ rs6838769 ]
For chromosome 4, 34844 SNPs pruned out, 5762 remaining
Scan region on chromosome 5 from [ rs9313223 ] to [ rs876154 ]
For chromosome 5, 36155 SNPs pruned out, 6117 remaining
Scan region on chromosome 6 from [ rs9392298 ] to [ rs12530134 ]
For chromosome 6, 41612 SNPs pruned out, 6898 remaining
Scan region on chromosome 7 from [ rs7456436 ] to [ rs1124425 ]
For chromosome 7, 32753 SNPs pruned out, 5564 remaining
Scan region on chromosome 8 from [ rs11780869 ] to [ rs6599566 ]
For chromosome 8, 31835 SNPs pruned out, 5367 remaining
Scan region on chromosome 9 from [ rs10814410 ] to [ rs9314655 ]
For chromosome 9, 28163 SNPs pruned out, 4811 remaining
Scan region on chromosome 10 from [ rs11252127 ] to [ rs11528930 ]
For chromosome 10, 33527 SNPs pruned out, 5731 remaining
Scan region on chromosome 11 from [ rs3802985 ] to [ rs12294124 ]
For chromosome 11, 31504 SNPs pruned out, 5327 remaining
Scan region on chromosome 12 from [ rs11063263 ] to [ rs11147298 ]
For chromosome 12, 30579 SNPs pruned out, 5143 remaining
Scan region on chromosome 13 from [ rs2762261 ] to [ rs17067959 ]
For chromosome 13, 23926 SNPs pruned out, 4037 remaining
Scan region on chromosome 14 from [ rs28842485 ] to [ rs10149476 ]
For chromosome 14, 20000 SNPs pruned out, 3436 remaining
Scan region on chromosome 15 from [ rs12905389 ] to [ rs4098905 ]
For chromosome 15, 18661 SNPs pruned out, 3115 remaining
Scan region on chromosome 16 from [ rs2541696 ] to [ rs4785775 ]
For chromosome 16, 19585 SNPs pruned out, 3308 remaining
Scan region on chromosome 17 from [ rs2396789 ] to [ rs7502442 ]
For chromosome 17, 17401 SNPs pruned out, 2971 remaining
Scan region on chromosome 18 from [ rs12455984 ] to [ rs12960632 ]
For chromosome 18, 18615 SNPs pruned out, 3185 remaining
Scan region on chromosome 19 from [ rs8100066 ] to [ rs10411093 ]
For chromosome 19, 12969 SNPs pruned out, 2242 remaining
Scan region on chromosome 20 from [ rs6139074 ] to [ rs6062363 ]
For chromosome 20, 15848 SNPs pruned out, 2678 remaining
Scan region on chromosome 21 from [ rs28971224 ] to [ rs10483083 ]
For chromosome 21, 8789 SNPs pruned out, 1503 remaining
Scan region on chromosome 22 from [ rs12157537 ] to [ rs3888396 ]
For chromosome 22, 9004 SNPs pruned out, 1527 remaining
Scan region on chromosome 23 from [ rs5939319 ] to [ rs669237 ]
For chromosome 23, 15760 SNPs pruned out, 2295 remaining
Scan region on chromosome 24 from [ rs11575897 ] to [ rs28715603 ]
For chromosome 24, 1409 SNPs pruned out, 0 remaining
Scan region on chromosome 25 from [ rs28503286 ] to [ rs2981828 ]
For chromosome 25, 393 SNPs pruned out, 80 remaining
Analysis finished: Fri Jun 27 15:46:24 2014
Also, the number of SNPs removed, as reported, is greater than the actual number of SNPs in the file: "Pruning complete. 749770 of 730525 variants removed." In reality, 658084 markers were removed, as listed in plink.prune.out.
Two log files are attached below. The same output is seen with the 27 June development build. The log file from Plink 1.07 is also attached for the same command.
------------------------------------------------------------------------------------------------------------------------------------------
PLINK v1.90b2p 64-bit (17 Jun 2014)
6 arguments: --bfile r-temp --indep 50 5 2
Hostname: ANDRES-PC8064
Working directory: D:\Sequence data\ref12-nam4\PLINK
Start time: Fri Jun 27 15:10:45 2014
Random number seed: 1403878245
32693 MB RAM detected; reserving 16346 MB for main workspace.
730525 variants loaded from .bim file.
8 people (0 males, 0 females, 8 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
Using 1 thread (no multithreaded calculations invoked).
Calculating allele frequencies... done.
Warning: Nonmissing nonmale Y chromosome genotype(s) present.
Total genotyping rate is 0.812604.
730525 variants and 8 people pass filters and QC.
Note: No phenotypes present.
Pruned 60901 variants from chromosome 1, leaving 18446744073709550202.
Pruned 59699 variants from chromosome 2, leaving 18446744073709549866.
Pruned 48744 variants from chromosome 3, leaving 18446744073709550302.
Pruned 41958 variants from chromosome 4, leaving 18446744073709550264.
Pruned 43460 variants from chromosome 5, leaving 18446744073709550428.
Pruned 49470 variants from chromosome 6, leaving 18446744073709550656.
Pruned 39690 variants from chromosome 7, leaving 18446744073709550243.
Pruned 38052 variants from chromosome 8, leaving 18446744073709550766.
Pruned 34054 variants from chromosome 9, leaving 18446744073709550536.
Pruned 40531 variants from chromosome 10, leaving 18446744073709550343.
Pruned 37716 variants from chromosome 11, leaving 18446744073709550731.
Pruned 36778 variants from chromosome 12, leaving 18446744073709550560.
Pruned 28808 variants from chromosome 13, leaving 18446744073709550771.
Pruned 24071 variants from chromosome 14, leaving 18446744073709550981.
Pruned 22605 variants from chromosome 15, leaving 18446744073709550787.
Pruned 23628 variants from chromosome 16, leaving 18446744073709550881.
Pruned 21081 variants from chromosome 17, leaving 18446744073709550907.
Pruned 22626 variants from chromosome 18, leaving 18446744073709550790.
Pruned 15754 variants from chromosome 19, leaving 18446744073709551073.
Pruned 18859 variants from chromosome 20, leaving 18446744073709551283.
Pruned 10590 variants from chromosome 21, leaving 18446744073709551318.
Pruned 10923 variants from chromosome 22, leaving 18446744073709551224.
Pruned 17896 variants from chromosome 23, leaving 159.
Pruned 1409 variants from chromosome 24, leaving 0.
Pruned 467 variants from chromosome 25, leaving 6.
Pruning complete. 749770 of 730525 variants removed.
Marker lists written to plink.prune.in and plink.prune.out .
End time: Fri Jun 27 15:10:54 2014
------------------------------------------------------------------------------------------------------------------------------------------
PLINK v1.90b2p 64-bit (17 Jun 2014)
6 arguments: --bfile r-temp --indep 50 5 2
Hostname: ANDRES-PC8064
Working directory: D:\Sequence data\ref12-nam4\PLINK
Start time: Fri Jun 27 15:14:56 2014
Random number seed: 1403878496
32693 MB RAM detected; reserving 16346 MB for main workspace.
730525 variants loaded from .bim file.
8 people (0 males, 0 females, 8 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
Using 1 thread (no multithreaded calculations invoked).
Calculating allele frequencies... done.
Warning: Nonmissing nonmale Y chromosome genotype(s) present.
Total genotyping rate is 0.819564.
730525 variants and 8 people pass filters and QC.
Note: No phenotypes present.
Pruned 59034 variants from chromosome 1, leaving 453.
Pruned 57387 variants from chromosome 2, leaving 562.
Pruned 46899 variants from chromosome 3, leaving 531.
Pruned 40294 variants from chromosome 4, leaving 312.
Pruned 41933 variants from chromosome 5, leaving 339.
Pruned 48088 variants from chromosome 6, leaving 422.
Pruned 38168 variants from chromosome 7, leaving 149.
Pruned 37015 variants from chromosome 8, leaving 187.
Pruned 32843 variants from chromosome 9, leaving 131.
Pruned 39001 variants from chromosome 10, leaving 257.
Pruned 36537 variants from chromosome 11, leaving 294.
Pruned 35607 variants from chromosome 12, leaving 115.
Pruned 27945 variants from chromosome 13, leaving 18.
Pruned 23253 variants from chromosome 14, leaving 183.
Pruned 21718 variants from chromosome 15, leaving 58.
Pruned 22779 variants from chromosome 16, leaving 114.
Pruned 20305 variants from chromosome 17, leaving 67.
Pruned 21668 variants from chromosome 18, leaving 132.
Pruned 15103 variants from chromosome 19, leaving 108.
Pruned 18309 variants from chromosome 20, leaving 217.
Pruned 10202 variants from chromosome 21, leaving 90.
Pruned 10537 variants from chromosome 22, leaving 18446744073709551610.
Pruned 17668 variants from chromosome 23, leaving 387.
Pruned 1409 variants from chromosome 24, leaving 0.
Pruned 483 variants from chromosome 25, leaving 18446744073709551606.
Pruning complete. 724185 of 730525 variants removed.
Marker lists written to plink.prune.in and plink.prune.out .
End time: Fri Jun 27 15:15:01 2014
------------------------------------------------------------------------------------------------------------------------------------------
@----------------------------------------------------------@
| PLINK! | v1.07 | 10/Aug/2009 |
|----------------------------------------------------------|
| (C) 2009 Shaun Purcell, GNU General Public License, v2 |
|----------------------------------------------------------|
| For documentation, citation & bug-report instructions: |
| http://pngu.mgh.harvard.edu/purcell/plink/ |
@----------------------------------------------------------@
Web-based version check ( --noweb to skip )
Recent cached web-check found... OK, v1.07 is current
+++ PLINK 1.9 is now available! See above website for details +++
Writing this text to log file [ plink.log ]
Analysis started: Fri Jun 27 15:44:01 2014
Options in effect:
--bfile r-temp
--indep 50 5 2
Reading map (extended format) from [ r-temp.bim ]
730525 markers to be included from [ r-temp.bim ]
Reading pedigree information from [ r-temp.fam ]
8 individuals read from [ r-temp.fam ]
0 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 0 controls and 8 missing
0 males, 0 females, and 8 of unspecified sex
Warning, found 8 individuals with ambiguous sex codes
These individuals will be set to missing ( or use --allow-no-sex )
Writing list of these individuals to [ plink.nosex ]
Reading genotype bitfile from [ r-temp.bed ]
Detected that binary PED file is v1.00 SNP-major mode
Before frequency and genotyping pruning, there are 730525 SNPs
8 founders and 0 non-founders found
707 SNPs with no founder genotypes observed
Warning, MAF set to 0 for these SNPs (see --nonfounders)
Writing list of these SNPs to [ plink.nof ]
Total genotyping rate in remaining individuals is nan
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 730525 SNPs
After filtering, 0 cases, 0 controls and 8 missing
After filtering, 0 males, 0 females, and 8 of unspecified sex
Performing LD-based pruning...
Writing pruned-in SNPs to [ plink.prune.in ]
Writing pruned-out SNPs to [ plink.prune.out ]
Scanning from chromosome 0 to XY
Skippng chromosome 0
Scan region on chromosome 1 from [ rs4477212 ] to [ rs12746903 ]
For chromosome 1, 50864 SNPs pruned out, 8623 remaining
Scan region on chromosome 2 from [ rs10195681 ] to [ rs12478296 ]
For chromosome 2, 49763 SNPs pruned out, 8186 remaining
Scan region on chromosome 3 from [ rs13060385 ] to [ rs10433653 ]
For chromosome 3, 40636 SNPs pruned out, 6794 remaining
Scan region on chromosome 4 from [ rs13125929 ] to [ rs6838769 ]
For chromosome 4, 34844 SNPs pruned out, 5762 remaining
Scan region on chromosome 5 from [ rs9313223 ] to [ rs876154 ]
For chromosome 5, 36155 SNPs pruned out, 6117 remaining
Scan region on chromosome 6 from [ rs9392298 ] to [ rs12530134 ]
For chromosome 6, 41612 SNPs pruned out, 6898 remaining
Scan region on chromosome 7 from [ rs7456436 ] to [ rs1124425 ]
For chromosome 7, 32753 SNPs pruned out, 5564 remaining
Scan region on chromosome 8 from [ rs11780869 ] to [ rs6599566 ]
For chromosome 8, 31835 SNPs pruned out, 5367 remaining
Scan region on chromosome 9 from [ rs10814410 ] to [ rs9314655 ]
For chromosome 9, 28163 SNPs pruned out, 4811 remaining
Scan region on chromosome 10 from [ rs11252127 ] to [ rs11528930 ]
For chromosome 10, 33527 SNPs pruned out, 5731 remaining
Scan region on chromosome 11 from [ rs3802985 ] to [ rs12294124 ]
For chromosome 11, 31504 SNPs pruned out, 5327 remaining
Scan region on chromosome 12 from [ rs11063263 ] to [ rs11147298 ]
For chromosome 12, 30579 SNPs pruned out, 5143 remaining
Scan region on chromosome 13 from [ rs2762261 ] to [ rs17067959 ]
For chromosome 13, 23926 SNPs pruned out, 4037 remaining
Scan region on chromosome 14 from [ rs28842485 ] to [ rs10149476 ]
For chromosome 14, 20000 SNPs pruned out, 3436 remaining
Scan region on chromosome 15 from [ rs12905389 ] to [ rs4098905 ]
For chromosome 15, 18661 SNPs pruned out, 3115 remaining
Scan region on chromosome 16 from [ rs2541696 ] to [ rs4785775 ]
For chromosome 16, 19585 SNPs pruned out, 3308 remaining
Scan region on chromosome 17 from [ rs2396789 ] to [ rs7502442 ]
For chromosome 17, 17401 SNPs pruned out, 2971 remaining
Scan region on chromosome 18 from [ rs12455984 ] to [ rs12960632 ]
For chromosome 18, 18615 SNPs pruned out, 3185 remaining
Scan region on chromosome 19 from [ rs8100066 ] to [ rs10411093 ]
For chromosome 19, 12969 SNPs pruned out, 2242 remaining
Scan region on chromosome 20 from [ rs6139074 ] to [ rs6062363 ]
For chromosome 20, 15848 SNPs pruned out, 2678 remaining
Scan region on chromosome 21 from [ rs28971224 ] to [ rs10483083 ]
For chromosome 21, 8789 SNPs pruned out, 1503 remaining
Scan region on chromosome 22 from [ rs12157537 ] to [ rs3888396 ]
For chromosome 22, 9004 SNPs pruned out, 1527 remaining
Scan region on chromosome 23 from [ rs5939319 ] to [ rs669237 ]
For chromosome 23, 15760 SNPs pruned out, 2295 remaining
Scan region on chromosome 24 from [ rs11575897 ] to [ rs28715603 ]
For chromosome 24, 1409 SNPs pruned out, 0 remaining
Scan region on chromosome 25 from [ rs28503286 ] to [ rs2981828 ]
For chromosome 25, 393 SNPs pruned out, 80 remaining
Analysis finished: Fri Jun 27 15:46:24 2014
Christopher Chang
Jun 27, 2014, 12:08:47 PM6/27/14
to plink2...@googlegroups.com
To clarify, is Plink 1.9 --indep just misreporting the number of SNPs pruned (but the actual .prune.in and .prune.out files are essentially identical to Plink 1.07's), or is --indep completely broken?
My initial attempts to replicate this issue have failed, so a test dataset that exhibits the problem would be very helpful.
My initial attempts to replicate this issue have failed, so a test dataset that exhibits the problem would be very helpful.
Christopher Chang
Jun 28, 2014, 11:20:56 PM6/28/14
to plink2...@googlegroups.com
Never mind, I've replicated this. This relates to a situation Plink 1.07 was handling incorrectly (singular covariance matrices); 1.9 beta 1 is... less incorrect, but there's more work to be done. Will try to post a proper patch soon.
Christopher Chang
Jul 1, 2014, 8:15:34 AM7/1/14
to plink2...@googlegroups.com
This should be fixed in the 1 Jul builds; let me know if you still see any anomalies.
On Friday, June 27, 2014 11:56:03 PM UTC+8, Kaustubh Adhikari wrote:
Reply all
Reply to author
Forward
0 new messages