Odd output format for bcftools isec

Question

[Begonia_pavonina]

I have 19 samples, and I wish to get the common loci shared by 8 of them. For this I use the code below:

    # List of VCF files 

vcf_files=(
        "Beg1_1.g.vcf" "Beg1_2.g.vcf" "Beg1_4.g.vcf" "Beg1_5.g.vcf"
        "Beg2_2.g.vcf" "Beg2_5.g.vcf" "Beg3_3.g.vcf" "Beg3_5.g.vcf"
        "Beg3_7.g.vcf" "Beg5_1.g.vcf" "Beg5_7.g.vcf" "Beg6_4.g.vcf"
        "Beg6_6.g.vcf" "Beg6_7.g.vcf" "Beg7_3.g.vcf" "Beg8_7.g.vcf"
        "Beg9_2.g.vcf" "Beg9_7.g.vcf" "hill.g.vcf" )

    # Compress VCF files 

for file in "${vcf_files[@]}"; do
        bgzip -c "$file" > "${file}.gz" done

    # Index the compressed VCF files 

for file in "${vcf_files[@]}"; do
        tabix -p vcf "${file}.gz" done

    # Intersect VCF files 

bcftools isec -n=8 "${vcf_files[@]/%/.gz}" > intersected.vcf

But looking at the result I realized that the intersected.vcf is odd. There is no vcf header, and the file is not really in vcf format. Would anyone know what I am doing wrong?

1185_polypolish 59005   C   <NON_REF>   1110010011011000000
1185_polypolish 59011   T   <NON_REF>   1011001011011000000
1185_polypolish 59020   A   <NON_REF>   1011001011011000000
1185_polypolish 59025   C   T,<NON_REF> 1010011011011000000
1185_polypolish 59028   G   A,<NON_REF> 1010011011011000000
1185_polypolish 59031   T   C,<NON_REF> 1010011011011000000
1185_polypolish 59061   T   C,<NON_REF> 1011001011011000000
1185_polypolish 59062   A   <NON_REF>   1011001011011000000
1104_polypolish 108092  T   G,<NON_REF> 0001000110011110010
1104_polypolish 108095  T   G,<NON_REF> 0001000110011110010

[GenoMax]

Check the README.txt file that should be present in the output folder. You also seem to be using gvcf's.

Answer 1

[Pierre Lindenbaum]

 T,<NON_REF> 

it looks like your trying to handle G.VCF files https://gatk.broadinstitute.org/hc/en-us/articles/360035531812-GVCF-Genomic-Variant-Call-Format . Bcftools isec is not the right tool to do this. You should use gatk combinegvcf and gatk genotypegvcfs

[Begonia_pavonina]

Thank you, I was completely unaware of the difference between VCF and GVCF file.