Samtools snpcalling

[zhkzhou]

1. What the maxmium samples in samtools snpcalling at one time?
2. How to merge the bcf files of multisamples. I mean combine several output bcf files in one(column combine). NOT the bcftools cat.
3. How to filter the snpcalling result, which paramters can be used to filter?
Many thanks for you answer.

[dharan]

Hi,
1. I have not tried SNP calling with more than 5 samples but I am sure it should be able to handle atleast 10.
The way I do my SNP calling in Samtools is I run mpileup for all my samples and parse the output to Bcf tools for creating a bcf file which you don't need to use bcf cat.
The bcf file that you will obtain is the raw file that you can filter using the samtools perl script vcfutils.pl.
For more information check this link: http://samtools.sourceforge.net/mpileup.shtml
Also you can try GATK tools for SNP calling.

Good Luck!

[swbarnes2]

Combining bcfs is not quite what you want to do, if you can help it. If at a locus, you have five samples with the reference allele, three samples with an alternate allele, and no coverage in two more, you want some indication that something is wrong for those two samples at that locus, but the bcf is unlikely to say anything about a region that has poor coverage, which might lead you to think that it has the reference allele.


You can combine a whole lot of samples in one mpileup call. The only limit is that it will impose a per sample depth cap, so that the total caps across all the samples adds up to 8000. So trying to run more than 400 samples at a time is not going to have enough coverage, but a few dozen should be fine.