When running: plink --vcf my.vcf --make-bed --out sex/plink An error was occured, please check the parameters!

[UndressK]

Hello,

I am getting an error when trying to run the software. Here is my code:

seGMM --vcf my.vcf \
              --input bam.file --alignment_format BAM \
              --reference_additional ~/resources/seGMM/ref_1000G_WES.txt \
              -t WES -o sex -g hg38

bam.file:
S1001 ~/data/S1001/S1001.bam

Any ideas why is failing?
Thank you!

[liusihan]

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!

[UndressK]

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! — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AH3HPTLBUCXNTYO7F7ARM5TXJUVWDANCNFSM6AAAAAAYZGSWRU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[UndressK]

I tried renaming the chromosomes by appending "chr" to CHROM column, but I am still getting the same error.

[liusihan]

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

[UndressK]

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 — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AH3HPTJES7A5XEWIZWMK47TXJ2SP5ANCNFSM6AAAAAAYZGSWRU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[liusihan]

Hi Andrés,

You need to activate the seGMM environment with conda and run the plink code in a shell window.

[UndressK]

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. — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AH3HPTKWVYCE636FW7HHEMTXJ7M43ANCNFSM6AAAAAAYZGSWRU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[liusihan]

Please test the code as follows:

(base) [shliu@admin1 ~]$ conda activate seGMM
(seGMM) [shliu@admin1 ~]$ ls
test.vcf
(seGMM) [shliu@admin1 ~]$ plink --vcf test.vcf --make-bed --out test0608 --allow-extra-chr
PLINK v1.90b6.21 64-bit (19 Oct 2020)          www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to test0608.log.
Options in effect:
  --allow-extra-chr
  --make-bed
  --out test0608
  --vcf test.vcf

257437 MB RAM detected; reserving 128718 MB for main workspace.
--vcf: test0608-temporary.bed + test0608-temporary.bim + test0608-temporary.fam
written.
145345 variants loaded from .bim file.
10 people (0 males, 0 females, 10 ambiguous) loaded from .fam.
Ambiguous sex IDs written to test0608.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 10 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.0529802.
145345 variants and 10 people pass filters and QC.
Note: No phenotypes present.
--make-bed to test0608.bed + test0608.bim + test0608.fam ... done.

[vikramadhithyaThotam22]

after that how to find the sex determination using seGMM tool