Using freebayes to call variants
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
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zhou_1228 •
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Hello zhou_1228 ,
can you tell me please which organism have a ploidy of 24 or 48?
fin swimmer
24 or 48 means there are 24 genomic DNAs in one well, and 48 genomic DNAs in another well.
-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