[Samtools-help] mpileup on a few SNPs?

[Tommy C. <tc...@sa...>]

To sam...@li...,

I'm trying to call 24 Sequenom SNPs across 57 crams. I was expecting it to take less than a minute, but it's been running for more than 15 minutes now. Is there a way to quickly call a small number of selected positions from indexed crams? This can be achieved with GATK, but samtools seems to be looping over the entire cram file or doing something else. Below is my command line. What do I need to add to make it faster and restrict the reading to the relevant reads in the bam file? Optionally I'll just extract the relevant reads from the cram files and generate a new set of crams to be used as input for mpileup.

$samtools mpileup -f $ref -l fluidigm.sites.txt -b cram.list -ug \
 | $bcftools call --ploidy GRCh38 -mO z -o $vcf

Thanks,
Tommy