Warning: Expected at least 2 parts in INFO entry...while using vcftools, what could be the reason

Question

[nidhisukhija5]

I used the following command and got warning Warning: Expected at least 2 parts in INFO entry......what could be the reason

vcftools --vcf /media/nidhi/deepu_hd/nidseq/filter/filgz2.vcf --out /media/nidhi/deepu_hd/nidseq/snp/snpgz2.vcf  --remove indels --recode-INFO-all

VCFtools - 0.1.16
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
    --vcf /media/nidhi/deepu_hd/nidseq/filter/filgz2.vcf
    --remove indels
    --recode-INFO-all
    --out /media/nidhi/deepu_hd/nidseq/snp/snpgz2.vcf

Warning: Expected at least 2 parts in INFO entry: ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
Warning: Expected at least 2 parts in INFO entry: ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
Excluding individuals in 'exclude' list
Error: Could not open Individual file:indels

Answer 1

[Ram]

Please read the manual. You used

--remove indels

You meant to use

--remove-indels

Run that and check if you still see the warnings.