samtools indels

[Robby]

Hi everyone,
I have a problem calling indels with samtools. Up to now, I called variants with the following command:
samtools pileup -vcf ref.fasta mapping.bam > raw_variants.var
and created the pileup file with:
samtools pileup -cf ref.fasta mapping.bam > mapping.pileup
After that I added the filter steps. But for my last samples I didn't receive any indels (just SNPs). In the mapping I can see indels, but neither in the pileup-file nor in the variance-files are indels. Are there any parameter to include/exclude indels? Or do I have to do anything different for Solid-reads mapped with Bioscope in comparision to Illumina-reads?

Thanks for your help!

[Heisman]

Have you thought about updating to the newer version of SAMtools that uses mpileup instead of pileup?

[Robby]

I tried with mpileup as well, but also in that file I can't see the indels

[Heisman]

Try these commands:

samtools-0.1.18/samtools mpileup -AB -ugf <reference_sequence> <aligned_file> | samtools-0.1.18/bcftools/bcftools view -bvcg -> <intermediate_file>

samtools-0.1.18/bcftools/bcftools view -e <intermediate_file> | samtools-0.1.18/bcftools/vcfutils.pl varFilter -D99999 > <variants.txt>