Clumping - plink1.9
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Stefano Onano
Mar 29, 2018, 4:26:23 PM3/29/18
to plink2-users
Hi, I'm doing a clumping on a variant list file filtered on chr22 as test, using a 1000g phase 3 binary file for the genotype input file.
$GenotypeBinaryFile has been generated with plink -make-bed from this vcf:
#CHROM POS ID REF ALT QUAL ...
22 16050075 chr22_16050075_A_G A G 100 ...
22 16050115 chr22_16050115_G_A G A 100 ...
22 16050213 chr22_16050213_C_T C T 100 ...
22 16050319 chr22_16050319_C_T C T 100 ...
22 16050527 chr22_16050527_C_A C A 100 ...
22 16050568 chr22_16050568_C_A C A 100 ...
22 16050607 chr22_16050607_G_A G A 100 ...
$InputFileTag.MOD.assoc:
CHR SNP BP A1 A2 ... P
22 chr22_32157225_C_G 32157225 C G ... 2.69738e-01
22 chr22_32157316_G_T 32157316 G T ... 4.70567e-01
22 chr22_32157480_T_C 32157480 T C ... 7.68571e-01
22 chr22_32157521_C_T 32157521 C T ... 4.39408e-01
22 chr22_32158129_G_T 32158129 G T ... 2.04889e-02
22 chr22_32158194_A_G 32158194 A G ... 4.09221e-01
plink
--bfile $GenotypeBinaryFileTag
--clump $InputFileTag.MOD.assoc
--clump-r2 0.08
--clump-verbose
--clump-annotate A1,OR
in the plink.log:
Random number seed: 1522350236
32013 MB RAM detected; reserving 16006 MB for main workspace.
1103547 variants loaded from .bim file.
503 people (0 males, 0 females, 503 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 503 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.999896.
1103547 variants and 503 people pass filters and QC.
Note: No phenotypes present.
--clump: 21 clumps formed from 152 top variants.
Results written to plink.clumped .
but in the plink.clumped there are only these lines without any variant annotations.
CHR F
22 1
(INDEX)
I've tryied also without "--clump-verbose" and "--clump-annotate A1,OR" but the outcome is similar:
CHR F
22 1
22 1
22 1
22 1
22 1
22 1
22 1
22 1
22 1
22 1
22 1
22 1
22 1
22 1
22 1
22 1
22 1
22 1
22 1
22 1
22 1
Any suggestion?
tnks
Stefano
Christopher Chang
Mar 29, 2018, 4:32:21 PM3/29/18
to plink2-users
Can you post the plink version string in the .log file?
Stefano Onano
Mar 29, 2018, 4:51:07 PM3/29/18
to plink2-users
PLINK v1.90b3.38 64-bit (7 Jun 2016)
Options in effect:
--bfile chr22.test.binary
--clump 1190.MOD.chr22.assoc
--clump-annotate A1,OR
--clump-r2 0.08
--clump-verbose
Christopher Chang
Mar 29, 2018, 4:56:07 PM3/29/18
to plink2-users
Ok. Try rerunning with a more recent build; if the problem remains, can you send me a test dataset to replicate with?
Stefano Onano
Mar 29, 2018, 4:57:41 PM3/29/18
to Christopher Chang, plink2-users
ok, I'll try!
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Stefano Onano
Apr 3, 2018, 10:39:10 AM4/3/18
to Christopher Chang, plink2-users
Hi Christopher, it works. Actually i realized there was a problem just with the visualization of the output file, but the file was correct. so, better.
thank you for your advices!
Shicheng Guo
Apr 3, 2018, 2:45:41 PM4/3/18
to plink2-users
Hi Stefano,
Can you share the script to transfer 1000 genome vcf to plink format?
I tried both plink --vcf and vcftools --plink, none of them works caused by strange error report.
One of errors is ./? something like that and when I try to remove these SNPs, there will be a '.' in the first line of missnps.
Thanks.
Shicheng
Christopher Chang
Apr 3, 2018, 2:58:18 PM4/3/18
to plink2-users
You’ll receive much better help if you actually post the .log file from a failed run, instead of using “strange error report” to describe something you’re unfamiliar with but which several people here probably understand.
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