我现在的问题是这样的

vcf文件转plink的格式

方法一

vcftools

[lyc@200server ~]$ vcftools --vcf Rice.recode.vcf --plink --out output

出错这样

VCFtools - 0.1.17

(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:

--vcf Rice.recode.vcf

--out output

--plink

Warning: Expected at least 2 parts in FORMAT entry: ID=RNC,Number=2,Type=Character,Description="Reason for No Call in GT: . = n/a, M = Missing data, P = Partial data, I = gVCF input site is non-called, D = insufficient Depth of coverage, - = unrepresentable overlapping deletion, L = Lost/unrepresentable allele (other than deletion), U = multiple Unphased variants present, O = multiple Overlapping variants present, 1 = site is Monoallelic, no assertion about presence of REF or ALT allele">

After filtering, kept 141 out of 141 Individuals

Writing PLINK PED and MAP files ...

Unrecognized values used for CHROM: Chr1 - Replacing with 0.

ls

ls

clear

Unrecognized values used for CHROM: Chr2 - Replacing with 0.

Expected at least 2 parts in FORMAT entry: ID=RNC,Number=2,Type=Character,Description="Reason for No Call in GT: . = n/a, M = Missing data, P = Partial data, I = gVCF input site is non-called, D = insufficient Depth of coverage, - = unrepresentable overlapping deletion, L = Lost/unrepresentable allele (other than deletion), U = multiple Unphased variants present, O = multiple Overlapping variants present, 1 = site is Monoallelic, no assertion about presence of REF or ALT allele">

Unrecognized values used for CHROM: Chr3 - Replacing with 0.

Unrecognized values used for CHROM: Chr4 - Replacing with 0.

Unrecognized values used for CHROM: Chr5 - Replacing with 0.

Unrecognized values used for CHROM: Chr6 - Replacing with 0.

Unrecognized values used for CHROM: Chr7 - Replacing with 0.

Unrecognized values used for CHROM: Chr8 - Replacing with 0.

Unrecognized values used for CHROM: Chr9 - Replacing with 0.

Unrecognized values used for CHROM: Chr10 - Replacing with 0.

Unrecognized values used for CHROM: Chr11 - Replacing with 0.

Unrecognized values used for CHROM: Chr12 - Replacing with 0.

Unrecognized values used for CHROM: ChrUn - Replacing with 0.

Unrecognized values used for CHROM: ChrSy - Replacing with 0.

Unrecognized values used for CHROM: chrC - Replacing with 0.

Done.

After filtering, kept 7186300 out of a possible 7186300 Sites

Run Time = 1647.00 seconds

[lyc@200server ~]$ ls

file.log output.ped prettify

file-temporary.bed output-temporary.bed Rice.recode.vcf

file-temporary.bim output-temporary.bim test

file-temporary.fam output-temporary.fam toy.map

LICENSE plink toy.ped

output.log plink_linux_x86_64_20201019.zip

output.map ppp

[lyc@200server ~]$

[lyc@200server ~]$ ls

file.log output.ped prettify

file-temporary.bed output-temporary.bed Rice.recode.vcf

file-temporary.bim output-temporary.bim test

file-temporary.fam output-temporary.fam toy.map

LICENSE plink toy.ped

output.log plink_linux_x86_64_20201019.zip

output.map ppp

[lyc@200server ~]$ clear

[lyc@200server ~]$ Expected at least 2 parts in FORMAT entry: ID=RNC,Number=2,Type=Character,Description="Reason for No Call in GT: . = n/a, M = Missing data, P = Partial data, I = gVCF input site is non-called, D = insufficient Depth of coverage, - = unrepresentable overlapping deletion, L = Lost/unrepresentable allele (other than deletion), U = multiple Unphased variants present, O = multiple Overlapping variants present, 1 = site is Monoallelic, no assertion about presence of REF or ALT allele">

-bash: 未预期的符号 `newline' 附近有语法错误

方法二plink

plink --vcf Rice.recode.vcf --recode --out file

plink --vcf Rice.recode.vcf --recode --out output --double-id

plink --vcf Rice.recode.vcf --recode --out output --const-fid family_id

都是一样的结果

773821 MB RAM detected; reserving 386910 MB for main workspace.

Error: Line 38 of .vcf file has a GT half-call.

Use --vcf-half-call to specify how these should be processed.

就无语

之前我的文件有这些

file.log LICENSE plink Rice.recode.vcf

file-temporary.bed output.log plink_linux_x86_64_20201019.zip test

file-temporary.bim output.map ppp toy.map

file-temporary.fam output.ped prettify toy.ped

现在是这些

file.log output.ped prettify

file-temporary.bed output-temporary.bed Rice.recode.vcf

file-temporary.bim output-temporary.bim test

file-temporary.fam output-temporary.fam toy.map

LICENSE plink toy.ped

output.log plink_linux_x86_64_20201019.zip

output.map ppp

然后看到了这些

image.png

https://www.cog-genomics.org/plink/1.9/input

然后我就重新安装了plink为plink2

http://www.cog-genomics.org/plink/2.0/

linux上安装Plink

https://blog.csdn.net/qq_40605470/article/details/108882992

但是又遇到了新的问题

[lyc@200server ~]$ plink2 --vcf Rice.recode.vcf --recode --out ccc

PLINK v2.00a3LM 64-bit Intel (2 Mar 2021) www.cog-genomics.org/plink/2.0/

(C) 2005-2021 Shaun Purcell, Christopher Chang GNU General Public License v3

Logging to ccc.log.

Options in effect:

--export ped

--out ccc

--vcf Rice.recode.vcf

Start time: Thu Mar 18 20:20:58 2021

773821 MiB RAM detected; reserving 386910 MiB for main workspace.

Using up to 80 threads (change this with --threads).

--vcf: 7146k variants scanned.

Error: Invalid chromosome code 'ChrUn' on line 7146662 of --vcf file.

(Use --allow-extra-chr to force it to be accepted.)

End time: Thu Mar 18 20:21:32 2021

然后发现文件又是临时文件

[lyc@200server ~]$ ls

ccc.log plink2

ccc-temporary.psam plink2_linux_x86_64_20210302.zip

file.log plink2.log

file-temporary.bed plink_linux_x86_64_20201019.zip

file-temporary.bim ppp

file-temporary.fam prettify

LICENSE Rice.recode.vcf

output.log test

output.map toy.map

output.ped toy.ped

output-temporary.bed transform.log

output-temporary.bim transform-temporary.bed

output-temporary.fam transform-temporary.bim

plink transform-temporary.fam

说明又出错了

所以，现在或许又要解决那一行的无效染色体

然后我就使用了--allow-extra-chr

[lyc@200server ~]$ plink2 --vcf Rice.recode.vcf --recode --out ccc --allow-extra-chr

PLINK v2.00a3LM 64-bit Intel (2 Mar 2021) www.cog-genomics.org/plink/2.0/

(C) 2005-2021 Shaun Purcell, Christopher Chang GNU General Public License v3

Logging to ccc.log.

Options in effect:

--allow-extra-chr

--export ped

--out ccc

--vcf Rice.recode.vcf

Start time: Fri Mar 19 16:31:21 2021

773821 MiB RAM detected; reserving 386910 MiB for main workspace.

Using up to 80 threads (change this with --threads).

--vcf: 7186300 variants scanned.

Error: Line 38 of --vcf file has a GT half-call.

Use --vcf-half-call to specify how these should be processed.

End time: Fri Mar 19 16:32:26 2021

哈，又回到了最初的起点

image.png

可是我看意思，plink2不应该有这个问题啊

[lyc@200server ~]$ plink2 --vcf Rice.recode.vcf --recode --out ccc --allow-extra-chr --vcf-half-call

PLINK v2.00a3LM 64-bit Intel (2 Mar 2021) www.cog-genomics.org/plink/2.0/

(C) 2005-2021 Shaun Purcell, Christopher Chang GNU General Public License v3

Logging to ccc.log.

Options in effect:

--allow-extra-chr

--export ped

--out ccc

--vcf Rice.recode.vcf

--vcf-half-call

Start time: Fri Mar 19 16:33:16 2021

Error: Missing --vcf-half-call argument.

For more info, try "plink2 --help " or "plink2 --help | more".

[lyc@200server ~]$ plink --vcf Rice.recode.vcf --allow-extra-chr --recode --vcf-half-call'missing' --out eee

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 eee.log.

Options in effect:

--allow-extra-chr

--out eee

--recode

--vcf Rice.recode.vcf

--vcf-half-callmissing

Error: Unrecognized flag ('--vcf-half-callmissing').

For more information, try "plink --help " or "plink --help | more".

发现原来是因为少了空格

[lyc@200server ~]$ plink --vcf Rice.recode.vcf --allow-extra-chr --recode --vcf-half-call 'haploid' --out eee

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 eee.log.

Options in effect:

--allow-extra-chr

--out eee

--recode

--vcf Rice.recode.vcf

--vcf-half-call haploid

773821 MB RAM detected; reserving 386910 MB for main workspace.

--vcf: eee-temporary.bed + eee-temporary.bim + eee-temporary.fam written.

7186300 variants loaded from .bim file.

141 people (0 males, 0 females, 141 ambiguous) loaded from .fam.

Ambiguous sex IDs written to eee.nosex .

Using 1 thread (no multithreaded calculations invoked).

Before main variant filters, 141 founders and 0 nonfounders present.

Calculating allele frequencies... done.

Total genotyping rate is 0.878065.

7186300 variants and 141 people pass filters and QC.

Note: No phenotypes present.

--recode ped to eee.ped + eee.map ... done.

[lyc@200server ~]$ plink --file eee --allow-extra-chr --make-bed --out rice

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 rice.log.

Options in effect:

--allow-extra-chr

--file eee

--make-bed

--out rice

773821 MB RAM detected; reserving 386910 MB for main workspace.

.ped scan complete (for binary autoconversion).

Performing single-pass .bed write (7186300 variants, 141 people).

--file: rice-temporary.bed + rice-temporary.bim + rice-temporary.fam written.

7186300 variants loaded from .bim file.

141 people (0 males, 0 females, 141 ambiguous) loaded from .fam.

Ambiguous sex IDs written to rice.nosex .

Using 1 thread (no multithreaded calculations invoked).

Before main variant filters, 141 founders and 0 nonfounders present.

Calculating allele frequencies... done.

Total genotyping rate is 0.878065.

7186300 variants and 141 people pass filters and QC.

Note: No phenotypes present.

--make-bed to rice.bed + rice.bim + rice.fam ... done.

这回终于对了

image.png

但问题是第一种转的，不知道应该是哪一种

image.png

我直接用了

我发现用plink2依然也还是这个问题，我看到一个答案貌似说是因为版本还不够新，今年初的那个改进版本或许可以修正这个问题

[lyc@200server ~]$ plink2 --vcf Rice.recode.vcf --allow-extra-chr --make-bed --out test

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 test.log.

Options in effect:

--allow-extra-chr

--make-bed

--out test

--vcf Rice.recode.vcf

773821 MB RAM detected; reserving 386910 MB for main workspace.

Error: Line 38 of .vcf file has a GT half-call.

Use --vcf-half-call to specify how these should be processed.