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When running: plink --vcf my.vcf --make-bed --out sex/plink An error was occured, please check the parameters! #7
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Hello, Was there any presence of abnormal chromosomes other than chr1 to chr22, chrX, and chrY in your VCF file? It seems that the issue with seGMM arises when the input VCF contains ALT contigs such as chrX_KI270880v1_alt. Please refer to similar questions in #6. Thank you! |
Thanks for your reply!
My chromosomes are named without the "chr" in the vcf file, so just: "1",
"2",..."X","Y","MT". I have some alternative chromosome contigs, but only
in the header: "##contig=<ID=KI270728.1,length=1872759>" There does not
seem to be variants called in the rest of the vcf files..
Will it fail also if chromosomes are not named like "chr1","chr2"..?
Andrés C.
…On Mon, 5 Jun 2023 at 03:01, Sihan Liu ***@***.***> wrote:
Hello,
Was there any presence of abnormal chromosomes other than chr1 to chr22,
chrX, and chrY in your VCF file? It seems that the issue with seGMM arises
when the input VCF contains ALT contigs such as chrX_KI270880v1_alt. Please
refer to similar questions in #6
<#6>.
Thank you!
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I tried renaming the chromosomes by appending "chr" to CHROM column, but I am still getting the same error. |
Hi Andrés, seGMM has the capability to predict sex using a VCF file that contains chromosomes named with or without the "chr" prefix. If possible, could you upload the vcf file you used or try the plink code as follows: plink --vcf vcffile --make-bed --out output --allow-extra-chr. Sihan |
Hi Sihan,
thanks for your reply! sorry, where exactly should I add that line of code?
…On Tue, 6 Jun 2023 at 05:52, Sihan Liu ***@***.***> wrote:
Hi Andrés,
seGMM has the capability to predict sex using a VCF file that contains
chromosomes named with or without the "chr" prefix. If possible, could you
upload the vcf file you used or try the plink code as follows: plink --vcf
vcffile --make-bed --out output --allow-extra-chr.
Sihan
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Hi Andrés, You need to activate the seGMM environment with conda and run the plink code in a shell window. |
plink --vcf vcffile --make-bed --out output --allow-extra-chr
plink: unknown option "--vcf"
plink: unknown option "--make-bed"
plink: unknown option "--out"
Andrés C.
…On Wed, 7 Jun 2023 at 03:50, Sihan Liu ***@***.***> wrote:
Hi Andrés,
You need to activate the seGMM environment with conda and run the plink
code in a shell window.
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Please test the code as follows:
|
after that how to find the sex determination using seGMM tool |
Hello,
I am getting an error when trying to run the software. Here is my code:
bam.file:
S1001 ~/data/S1001/S1001.bam
Any ideas why is failing?
Thank you!
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