bcftools view to failed reader data

Question

[Jihyun]

It's so confused for data editing with vcftools - bcftools fusion preprocessing.

I want to view all results in bcftools, vcftool and zcat when I typing command, but it doesn't work.

for example, i want to see same results with

1. bcftools view input.file | less

[environment]$ bcftools view input.vcf.gz | le Failed to read from input.vcf.gz: unknown file type

1. vcftools --gzvcf input.file --recode --recode-INFO-all --stdout | less

fileDate=19/07/2023 - 16:10:54

  2 ##source=SHAPEIT5 phase_common 1.1
  3 ##contig=<ID=1,IDX=0>
  4 ##INFO=<ID=AC,Number=A,Type=Integer,Description="ALT allele count">
  5 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Number of alleles">
  6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Phased genotypes">
  7 #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Sam1 Sam2 Sam3 ...
  8 1       102988  rsID    C       A       nan     .       AC=13;AN=198    GT      0|0     0|0     0|0     0|0     0|0    

1. zcat input.file | less

fileDate=19/07/2023 - 16:10:54

  2 ##source=SHAPEIT5 phase_common 1.1
  3 ##contig=<ID=1,IDX=0>
  4 ##INFO=<ID=AC,Number=A,Type=Integer,Description="ALT allele count">
  5 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Number of alleles">
  6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Phased genotypes">
  7 #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Sam1 Sam 2 Sam3...
  8 1       102988  rsID    C       A       nan     .       AC=13;AN=198    GT      0|0     0|0     0|0     0|0     0|0   

vcftools --gzvcf and zcat command works well (provide same results) but bcftools just omit the error : unknown file type

How do I solve this problem? In other input file, command sets works well and bcftools doesn't failed for read.

Thank you for attention.

Answer 1

[DBScan]

Your vcf file doesnt contain the fileformat header, which is necessary.

[Jihyun]

Oh, Thank you for answer. Would you explain the solution for this problem? Could I just solved with editing "##fileformat=VCFv4.2 \n ##FILTER=<ID=PASS,Description="All filters passed">\n" in the first and second line?

[DBScan]

You can try that, but where did you get these VCFs from?

[Jihyun]

Well, I just filtering bcf and coverted it to vcf.gz for extracting MAF 0.01, and these files popped up... bcf was from after impute process, and vcftools omitted error as index : "inputfile" is in a format that cannot be usefully indexed. Here is the command

(After impute process) bcftools view input.bcf -Oz -o input.refine.vcf.gz

vcftools --gzvcf input.refine.vcf.gz --maf 0.01 --recode --recode-INFO-all --stdout | bgzip -c > output.vcf.gz && tabix -p vcf output.vcf.gz

[Jihyun]

Oh, I found the answer. Maybe direct filtering with bcf to vcf.gz output take the error easily! (Just my opinion, error message doesn't answer anything..)

Before I do bcf -> vcf.gz -> vcf.gz (maf filtering), but I do bcf -> vcf.gz (maf filtering) in this time.