VCF Tools converting

Question

[storm1907]

Hello, I am in need to convert vcf to fasta. Previous topics did not seem to resolve this type of problem

I have this code, but when trying to do bgzip and tabix commands, i afterwards get error like "the input file is not BGZF" and "Broken VCF header, no column names?" Any help will be appreciated

#!bin/bash
module load bio/vcftools/0.1.17
module load bio/samtools/1.10

export inpath=/dir

export outpath=/dir
mkdir -p $outpath
chmod u+rwx $outpath
export reference=/ref
$reference
for file in $inpath/* ;
do
        bname=$(basename $file)
        echo "base name is $bname"
        bfile=$outpath/$bname".bgz"
        tabfile=$outpath/$bname".tabix"
        outfile=$outpath/$bname".fasta"
        bgzip $file $bfile
        cd $outpath
        tabix -f $bfile > $tabfile
        cat $reference | vcf-consensus $tabfile > $outfile
done

[Ram]

You're using the bgzip command wrong. You're also not giving tabix the preset to use, plus using the command itself wrong. Fix those and you should be fine. Read the bgzip/tabix manuals.

[storm1907]

Thank, you, fixed

for file in $inpath/*.filtered ;
do
        echo $file
        bname=$(basename $file)
        echo "base name is $bname"
        bfile=$inpath/$bname".gz"
        outfile=$outpath/$bname".fasta"
        bgzip -c $file > $bfile
        tabix -p vcf $bfile
        cat $reference | vcf-consensus $bfile > $outfile
done

but the next problem is: I get output fasta file with correct sample name in file's title, and reference sequence name inside the file:

<nc_xxx> <sequence>

Any suggestions, why is that? :o

[Ram]

Is that output not how you expect it to be? What do you expect and what are you getting?

[storm1907]

I would like to see sample's name in the very begginning of file. Not reference sequence's name

[Ram]

That seems to be a custom requirement, which may not be addressed by vcf-consensus. You should be able to use awk or bioawk to add a line containing the FILENAME.

[storm1907]

Thank you! I also had an idea, that vcf consensus might be supposed for generating multi-fasta. Because at the moment I am obtaining only single fasta files, which should be concatenated

[Ram]

Try switching to bcftools consensus. vcftools is obsolete, I think.