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. ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
