How samtools mpileup uses paired end data to determine SNP phasing
Hi all,
I am mapping paired end reads to a reference using bowtie2. Then, the samtools mpileup command creates a .bcf file, which I can convert to a .vcf file using the bcftools view command. Looking at this .vcf file, I see that it has SNP phasing information (aka which particular SNP variants are linked to each other).
What I'm wondering is this: is the SNP phasing information in this file limited to only SNPs that occur within a given read? Or does the program use paired end information to give me SNP linkage information over a longer distance?
Thanks for any insights. I haven't been able to track down this information anywhere else.
I am mapping paired end reads to a reference using bowtie2. Then, the samtools mpileup command creates a .bcf file, which I can convert to a .vcf file using the bcftools view command. Looking at this .vcf file, I see that it has SNP phasing information (aka which particular SNP variants are linked to each other).
What I'm wondering is this: is the SNP phasing information in this file limited to only SNPs that occur within a given read? Or does the program use paired end information to give me SNP linkage information over a longer distance?
Thanks for any insights. I haven't been able to track down this information anywhere else.