NO indel output from Samtools by using nearly default settings

[wwmm933]

Hi,

I mapped a paired-end sequencing by BWA with default settings and then called variants by Samtools with settings as follows.

samtools mpileup -ABuf hg18_genome.fna ${file}/${file}-sorted.bam | bcftools view -p 0.99 -bvcg - > ${file}/${file}-var.raw.bcf
bcftools view ${file}/${file}-var.raw.bcf | vcfutils.pl varFilter -d8 -D10000 -11e-5 -20 -41e-7 > ${file}/${file}-var.flt.vcf


However, I cannot get any indel output for the sample. Is there anything wrong with the parameters I set here (BWA or Samtools)?

Thanks!

[ekg]

What do you get with other snp+indel methods (e.g. freebayes or GATK)?