strange behavior in vcftools

[diego diaz]

Hi all,

I want to split my VCF file into two files, one with SNPs and another with INDELs. To that I am using VCF tools, with the following sentences:

# to keep only SNPs
vcftools --vcf myvariants.vcf --remove-indels --recode-INFO-all --out only_SNPs --recode

# to keep only INDELs
vcftools --vcf myvariants.vcf --keep-only-indels --recode-INFO-all --out only_INDELs --recode

but when I check the files, I get this:

INDELs:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
CM003279.1      1274    C       A       999     .
CM003279.1      3637    A       C       157     .
CM003279.1      3788    GCCCC   GCCCCC  130     .
CM003279.1      3879    A       C       999     .
.
.
.

SNPs:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
CM003279.1      25370   TAAA    TAA     999     .
CM003279.1      75537   TACAC   TAC     999     .
CM003279.1      77780   ACATCA  ACA     999     .
CM003279.1      3177577 CTTT    CTT     999     .
.
.
.

The splitting process doesn't make any sense, I have SNPs and INDELs in both files (I didn't add the genotype data here because it would be very difficult trying to read it)

In attachment the firts lines of my original VCF file.

I am pretty sure that the problem comes from my VCF file, not from vcftools, but I can't see the problem.

is there a tool to check if a vcf file is malformed?

Thanks in advance

[diego diaz]

I forgot to mention that the variants were called in the scaffolds not in the chromosomes, then I had to code a custom script to transform scaffolds coordinates into chromosomes coordinates, maybe during the process I forgot to put something but I can't see it.