Failed to open var.raw.bcf: unknown file type
Hi, I used the following commands to call SNPs
samtools merge ${1}/all.sorted.dedup.bam ${1}/*.sorted.dedup.bam
samtools index ${1}/all.sorted.dedup.bam
samtools faidx $2
samtools mpileup -uf $2 ${1}/all.sorted.dedup.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
but unfortunately, I got the following error:
[warning] samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future.
[mpileup] 4 samples in 1 input files
view: invalid option -- 'b'
About: VCF/BCF conversion, view, subset and filter VCF/BCF files.
Usage: bcftools view [options] <in.vcf.gz> [region1 [...]]
...
Failed to open var.raw.bcf: unknown file type
What did I miss?
Thank you in advance,
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