Using freebayes to call variants

Question

[zhou_1228]

I am using freebayes package to call SNPs from reads generated from NGS. It works well when I ran samples with 24 genome copies, however, the program got killed when I process samples with 48 genome copies using a local PC or it took about 10 hours to finish one sample when I ran it on a cluster. I want to know if I use the correct parameters in freebayes command. Thank you.

The command I use for sample with 24 genome copies:

freebayes -f GMN.fasta -p 24 --use-best-n-alleles 4 --pooled-discrete P1-WE02.sorted.bam >P1-WE02.vcf

The command I use for sample with 48 genome copies:

freebayes -f GMN.fasta -p 48 --use-best-n-alleles 4 --pooled-discrete P3-WA02.sorted.bam >P3-WA02.vcf

[finswimmer]

Hello zhou_1228 ,

can you tell me please which organism have a ploidy of 24 or 48?

fin swimmer

[zhou_1228]

24 or 48 means there are 24 genomic DNAs in one well, and 48 genomic DNAs in another well.

[nadiabeg.comsats]

-p is basically the ploidy. you have mentioned -p 48 means your samples have 48 genome copies. see this link for detailed explanation: https://github.com/ekg/freebayes