rwdavies
commented
2 years ago What version is this? I fixed a bug recently that led to similar issues. Assuming this is the previous version, I’m hoping the new version fixes this issue?
On Thu, 19 Aug 2021 at 02:21, Mirror-fish @.***> wrote:
Hello! I was doing 0.1x QUILT test using 1KG ref panel. This is the QUILT command:
QUILT.R --outputdir ./no_map_chr3 --chr chr3 --regionStart=180000000 --regionEnd=190000000 --buffer=12500 --bamlist=./bam0.1.list --reference_haplotype_file=./chr3.hap.gz --reference_legend_file=./chr3.legend.gz --nGen=10 \
And when I got the vcf file, trying to recode it into traw using Plink 2.0:
plink2 --recode A-transpose --vcf ./quilt.chr3.180000000.190000000.vcf.gz dosage=DS --const-fid 0 --set-all-var-ids chr@:# --out ./quilt_0.1x_1kg
An error happened:
Error: Line 672 of --vcf file has an invalid DS field.
Then I found I line 672 a variant which DS score is 2.001:
chr3 180392795 . G A . PASS EAF=0.98927;INFO_SCORE=0.07682;HWE=1.00e+00;ERC=3.99895;EAC=0.00035;PAF=0.99991 GT:GP:DS:HD 1|1:0.000,-0.001,1.001:2.001:1.002,1.000
I wonder how could this happen and how can I save it? Thanks.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/rwdavies/QUILT/issues/5, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB7I36JHPNVAX5IGDITSZDTT5SPHRANCNFSM5CNQHUQQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email .
Mirror-fish
Hello! I was doing 0.1x QUILT test using 1KG ref panel. This is the QUILT command:
And when I got the vcf file, trying to recode it into traw using Plink 2.0:
An error happened:
Then I found I line 672 a variant which DS score is 2.001:
I wonder how could this happen and how can I save it? Thanks.