question

[Griz054]

I could have sent an e-mail but I figured I'd ask the question here. I'm working with some folks that read my article about this entire process. One question that came up - in the script why didn't you just use the vcf to populate the data instead of grabbing the larger bam file?

[tkrahn]

Sorry for my late reply. The VCF may not tell me if a certain SNP is covered by sequencing reads. It may be covered by reads and just match the reference sequence or it may not be covered meaning a nocall.

So you'd at least need additional information from a BED file. Yet the BED file doesn't tell you the quality of the reads at each position, it just defines sections of the genome that are defined trust-worthy. This may have its quirks if just a single base in the middle of a BED region has quality issues. So using BED files comes with a lot of complicated questions. Therefore I have decided that the cleanest way is to directly score the SNPs from the BAM file.

[Griz054]

Thank you. I knew you had a reason. I just couldn't tell him what it was.

Jim "Griz" Adams

On May 5, 2017 2:55 PM, "tkrahn" notifications@github.com wrote:

Sorry for my late reply. The VCF may not tell me if a certain SNP is covered by sequencing reads. It may be covered by reads and just match the reference sequence or it may not be covered meaning a nocall.

So you'd at least need additional information from a BED file. Yet the BED file doesn't tell you the quality of the reads at each position, it just defines sections of the genome that are defined trust-worthy. This may have its quirks if just a single base in the middle of a BED region has quality issues. So using BED files comes with a lot of complicated questions. Therefore I have decided that the cleanest way is to directly score the SNPs from the BAM file.

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