vfc格式linux,2021-03-17 在linux上将vcf文件转plink的格式bed,bim,fam

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 val