I'm trying to get heterozygous SNPs from illumina DNA sequencing data.
I've used samtools/mpileup pipeline and have some questions about the options.
There are many posts related in the BAQ calculation. As known, the calculation is default and if the options -B is used, more SNPs could be detected (sacrificing the specificity). I've tested with my samples and the difference is almost ~2x or ~3x difference. (-uf vs -Buf, -Euf didn't make a big difference compared -uf)
Is there anyone with experience with -B -E and -I options?
Actually, we are not interested in INDELs so I thought that the option -I could be used for ignoring INDELs calling.
But when I compared the results (for heterozygous SNPs) with -I and without -I, many detected heterozygous SNPs in the results with -I option are actually the INDELs cases in the results without -I option. So is it better to ignore those SNPs, in another word, should I "not" use the -I option?
I really want to know the appropriate options for calling heterozygous SNPs.
I've used samtools/mpileup pipeline and have some questions about the options.
There are many posts related in the BAQ calculation. As known, the calculation is default and if the options -B is used, more SNPs could be detected (sacrificing the specificity). I've tested with my samples and the difference is almost ~2x or ~3x difference. (-uf vs -Buf, -Euf didn't make a big difference compared -uf)
Is there anyone with experience with -B -E and -I options?
Actually, we are not interested in INDELs so I thought that the option -I could be used for ignoring INDELs calling.
But when I compared the results (for heterozygous SNPs) with -I and without -I, many detected heterozygous SNPs in the results with -I option are actually the INDELs cases in the results without -I option. So is it better to ignore those SNPs, in another word, should I "not" use the -I option?
I really want to know the appropriate options for calling heterozygous SNPs.
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