BAQ in mpileup (SAMtools)
Hi, I am doing INDEL detection with mpileup/bcftools (version-0.1.18). First, I had problems to run my analysis for all genome and someone in this community suggested using the option -B, for the disable of BAQ computation, and then the analysis ran perfectly well for all chromosomes. I have many individuals to run.
But I have been reading about this BAQ computation, and I am not sure if is correct to disable this option for INDEL analysis. But, in other hand my analysis will not run with this computation...I did not have a huge number of INDELs, it seems ok.
The command line that I used
samtools mpileup –q20 –Q20 –AB -reference.fa file.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D99999 > var.flt.vcf
What do you think? Do I use -B or not? Why?
How BAQ will affect my analysis?
Is there another suggestion? Other better software to detect indels, like Dindel?
In the samtools page there is the comment: Currently the BAQ strategy is the only practical way to avoid the INDEL artifact in low-coverage multi-sample SNP calling.
Thanks,
Clarissa
But I have been reading about this BAQ computation, and I am not sure if is correct to disable this option for INDEL analysis. But, in other hand my analysis will not run with this computation...I did not have a huge number of INDELs, it seems ok.
The command line that I used
samtools mpileup –q20 –Q20 –AB -reference.fa file.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D99999 > var.flt.vcf
What do you think? Do I use -B or not? Why?
How BAQ will affect my analysis?
Is there another suggestion? Other better software to detect indels, like Dindel?
In the samtools page there is the comment: Currently the BAQ strategy is the only practical way to avoid the INDEL artifact in low-coverage multi-sample SNP calling.
Thanks,
Clarissa
