Question: Error in vcf, samtools
gravatar for wu.zhiqiang.1020
5.5 years ago by
United States
wu.zhiqiang.102020 wrote:

../software/samtools-1.1/samtools mpileup -uf ./ ./S_new_F4_pe_mem.sort.bam | ../software/bcftools-1.1/bcftools view -vcg - > S_new_F4_pe_mem.sort.bam.raw.bcf 

[mpileup] 1 samples in 1 input files

<mpileup> Set max per-file depth to 8000

[E::cg] unknown typ

What's the reason? please help.

I used the same version of samtools and bcftools



snp • 1.9k views
ADD COMMENTlink modified 4.5 years ago by Biostar ♦♦ 20 • written 5.5 years ago by wu.zhiqiang.102020
gravatar for Pierre Lindenbaum
5.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

you don't need to use bcftools view anymore:

samtools mpileup -ugf <ref.fa> <sample1.bam> <sample2.bam> <sample3.bam> | bcftools call -vmO z -o <study.vcf.gz>
ADD COMMENTlink written 5.5 years ago by Pierre Lindenbaum127k
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