How to remove variants with 3+ alleles present Plink1.9

Question

[ramshahaya]

Hi,

I had used GATK Haplotype caller to call Variant (SNP) on individual Samples. I had performed QC steps after converting VCF to plink format. Then

I was trying to merge using Plink1.9, But I am getting this error.

I would like to know how to remove variants with 3+ alleles?

/usr/bin/plink1.9 --cow --make-bed --merge-list myFile_150.txt --out mymerged_150
PLINK v1.90b6.22 64-bit (3 Nov 2020)           www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to mymerged_150.log.
Options in effect:
  --cow
  --make-bed
  --merge-list myFile_150.txt
  --out mymerged_150

64245 MB RAM detected; reserving 32122 MB for main workspace.
**Error: 2149 variants with 3+ alleles present.**
* If you believe this is due to strand inconsistency, try --flip with
  mymerged_150-merge.missnp.
  (Warning: if this seems to work, strand errors involving SNPs with A/T or C/G
  alleles probably remain in your data.  If LD between nearby SNPs is high,
  --flip-scan should detect them.)
* If you are dealing with genuine multiallelic variants, we recommend exporting
  that subset of the data to VCF (via e.g. '--recode vcf'), merging with
  another tool/script, and then importing the result; PLINK is not yet suited
  to handling them.
See https://www.cog-genomics.org/plink/1.9/data#merge3 for more discussion.

I had used --flip-scan option also , But I have got exact same error as I have mentioned above.

I would be grateful If I could help regarding this issue.

[Pierre Lindenbaum]

bcftools view and options -m and -M

-m, --min-alleles INT

    print sites with at least INT alleles listed in REF and ALT columns
-M, --max-alleles INT

    print sites with at most INT alleles listed in REF and ALT columns. Use -m2 -M2 -v snps to only view biallelic SNPs.

[ramshahaya]

HI,

I had tried to remove multiallele using bcftools

bcftools view --max-alleles 2 --min-alleles 2 23K.vcf.gz -o 23K_bi.vcf.gz -Oz 

Then I had converted VCF file to plink and try to merge, But It still throws this error.

/usr/bin/plink1.9 --cow --make-bed --merge-list myFile_150.txt --out mymerged_150 
PLINK v1.90b6.22 64-bit (3 Nov 2020)           www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to mymerged_150.log.
Options in effect:
  --cow
  --make-bed
  --merge-list myFile_150.txt
  --out mymerged_150

64245 MB RAM detected; reserving 32122 MB for main workspace.
Error: 6262 variants with 3+ alleles present.
* If you believe this is due to strand inconsistency, try --flip with
  mymerged_150-merge.missnp.
  (Warning: if this seems to work, strand errors involving SNPs with A/T or C/G
  alleles probably remain in your data.  If LD between nearby SNPs is high,
  --flip-scan should detect them.)
* If you are dealing with genuine multiallelic variants, we recommend exporting
  that subset of the data to VCF (via e.g. '--recode vcf'), merging with
  another tool/script, and then importing the result; PLINK is not yet suited
  to handling them.
See https://www.cog-genomics.org/plink/1.9/data#merge3 for more discussion.

It would be extremely appreciable If I could get any suggestions regarding my Query.

Answer 1

[Jingjingzhang]

Has anyone resolved this issue?