Error in vcf, samtools
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6.5 years ago

../software/samtools-1.1/samtools mpileup -uf ./S.int.fas ./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 • 2.1k views
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Entering edit mode
6.5 years ago

you don't need to use bcftools view anymore: http://www.htslib.org/workflow/#mapping_to_variant

samtools mpileup -ugf <ref.fa> <sample1.bam> <sample2.bam> <sample3.bam> | bcftools call -vmO z -o <study.vcf.gz>
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