Error in vcf, samtools

../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 type

What's the reason? please help.

I used the same version of samtools and bcftools

snp

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updated 4.5 years ago by Ram

• written 11.8 years ago by wu.zhiqiang.1020 •

1 answer

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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written 11.8 years ago by Pierre Lindenbaum

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