Hello,
For a start your bgzip command looks wrong. You probably want something like
this:
bgzip -c $file > $bfile
If that doesn't work, let me know what error messages/output you are getting.
Regards,
Andrew
________________________________________
From: Baiba Alksere <baiba.alks...@gmail.com>
Sent: 12 October 2020 08:25:02
To: samtools-help@lists.sourceforge.net
Subject: [Samtools-help] tabix and bgzip [EXT]
Hello,
I have problem with VCFtools running
I have code like this, but tabix is not recognizing input file as bgzf
(however, i am bgzipping it)
#!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
--
Best regards
Baiba Alkšere
--
The Wellcome Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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