**360**wrote:

Hi All,

I have ~ 200.Idat files from Illumina MEGAEx Genotyping array. I have done QCing using Plink and removed ambiguous samples. Next, i converted the .bam,.bim and .fim files into VCF using plink recode option.

When I try to determine and fix strand orientation using a +fixref plugin of BCFtools, it's showing 100% ref missmatch (I am using ref fasta from here)

Please let me know where I am going wrong or how to interpret this. My commands are:

```
bcftools +fixref GArray_qcd.vcf -- -f hg38.fa
```

And the output is as follows:

```
bcftools +fixref Genotypearray_qcd.vcf -- -f hg38.fa
[E::faidx_fetch_seq] The sequence "1" not found
Ignoring sequence "1"
[E::faidx_fetch_seq] The sequence "2" not found
Ignoring sequence "2"
[E::faidx_fetch_seq] The sequence "3" not found
Ignoring sequence "3"
[E::faidx_fetch_seq] The sequence "4" not found
Ignoring sequence "4"
[E::faidx_fetch_seq] The sequence "5" not found
Ignoring sequence "5"
[E::faidx_fetch_seq] The sequence "6" not found
Ignoring sequence "6"
[E::faidx_fetch_seq] The sequence "7" not found
Ignoring sequence "7"
[E::faidx_fetch_seq] The sequence "8" not found
Ignoring sequence "8"
[E::faidx_fetch_seq] The sequence "9" not found
Ignoring sequence "9"
[E::faidx_fetch_seq] The sequence "10" not found
Ignoring sequence "10"
[E::faidx_fetch_seq] The sequence "11" not found
Ignoring sequence "11"
[E::faidx_fetch_seq] The sequence "12" not found
Ignoring sequence "12"
[E::faidx_fetch_seq] The sequence "13" not found
Ignoring sequence "13"
[E::faidx_fetch_seq] The sequence "14" not found
Ignoring sequence "14"
[E::faidx_fetch_seq] The sequence "15" not found
Ignoring sequence "15"
[E::faidx_fetch_seq] The sequence "16" not found
Ignoring sequence "16"
[E::faidx_fetch_seq] The sequence "17" not found
Ignoring sequence "17"
[E::faidx_fetch_seq] The sequence "18" not found
Ignoring sequence "18"
[E::faidx_fetch_seq] The sequence "19" not found
Ignoring sequence "19"
[E::faidx_fetch_seq] The sequence "20" not found
Ignoring sequence "20"
[E::faidx_fetch_seq] The sequence "21" not found
Ignoring sequence "21"
[E::faidx_fetch_seq] The sequence "22" not found
Ignoring sequence "22"
[E::faidx_fetch_seq] The sequence "23" not found
Ignoring sequence "23"
[E::faidx_fetch_seq] The sequence "24" not found
Ignoring sequence "24"
[E::faidx_fetch_seq] The sequence "25" not found
Ignoring sequence "25"
[E::faidx_fetch_seq] The sequence "26" not found
Ignoring sequence "26"
# SC, guessed strand convention
SC TOP-compatible 1
SC BOT-compatible 1
# ST, substitution types
ST A>C 0 -nan%
ST A>G 0 -nan%
ST A>T 0 -nan%
ST C>A 0 -nan%
ST C>G 0 -nan%
ST C>T 0 -nan%
ST G>A 0 -nan%
ST G>C 0 -nan%
ST G>T 0 -nan%
ST T>A 0 -nan%
ST T>C 0 -nan%
ST T>G 0 -nan%
# NS, Number of sites:
NS total 26
NS ref match 0 0.0%
NS ref mismatch 26 100.0%
NS skipped 0
NS non-ACGT 0
NS non-SNP 0
NS non-biallelic 0
```

Thanks a lot,

Dave!