[Samtools-help] Calling SNPs with SAMtools and BCFtools

[p. <pe...@ga...>]

Hi,

I want to call SNPs with SAMtools and BCFtools.

It works with samtools version 0.1.19, but it doesn't work with samtools and bcftools version 1.3.1 and doesn't show any error.

The command with version 0.1.19:
samtools mpileup -C50 -q25 -uf REF.fasta merge.bam | bcftools view -bvcg - > merge.bcf

The command with version 1.3.1:
samtools mpileup -C50 -q25 -uf REF.fasta merge.bam | bcftools view -Ob -g^miss - > merge.bcf

How can I solve the problem with version 1.3.1?
Thanks.