Hi everyone.
1. I tried to call the snps using both mpileup and pileup.
There is more differences in snps calling numbers.
I found that mpileup give me less snps compared too pileup which produce lots of snps calling.
eg pileup = about 10 K snps while mpileup = about 800 snps
i run using this command
samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
is using mpileup is more thorough compared to pileup?
btw, i call the snps from rice data.
2. can anyone here explain how can i make use the genotype data that present in vcf 'FORMAT' ? I read already in the documentation but not really understand.
Thanks all!
1. I tried to call the snps using both mpileup and pileup.
There is more differences in snps calling numbers.
I found that mpileup give me less snps compared too pileup which produce lots of snps calling.
eg pileup = about 10 K snps while mpileup = about 800 snps
i run using this command
samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
is using mpileup is more thorough compared to pileup?
btw, i call the snps from rice data.
2. can anyone here explain how can i make use the genotype data that present in vcf 'FORMAT' ? I read already in the documentation but not really understand.
Thanks all!
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