mpileup indel problem

[Hit]

Hi, I tried to use samtools mpileup followed by bcftools to call SNPs and indels. When using the example command in samtools website, the results seem fine, and both SNPs and indels were called fine. Here are the command lines I used (I have only one sample):

samtools mpileup -ugf ref.fa aln1.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf

When I tried to use "-m 1796" in the mpileup step, no indels were called in the final var.flt.vcf file. Everything is the same except adding "-m 1796":

samtools mpileup -m 1796 -ugf ref.fa aln1.bam | bcftools view -bvcg - > var.raw.bcf


Could anyone tell me whether to use "-m 1796" and why this happen? I thought "-m 1796" is to remove reads unmapped, not primary alignment, read fails platform/vendor quality checkes, and read is PCR or optical duplicate. But why if using "-m 1796", there was no indel left?

[swbarnes2]

Looking at the samtools v 1.13 mpileup help

-m INT minimum gapped reads for indel candidates [1]

Looking at the help for the view command

-F INT filtering flag, 0 for unset [0]

That's what you want.