SAMtools mpileup

The SAMtools mpileup utility provides a summary of the coverage of mapped reads on a reference sequence at a single base pair resolution. In addition, the output from mpileup can be piped to BCFtools to call genomic variants. I'm currently working with some Sanger sequenced PCR products, which I would like to call variants on....

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VCF concordance

I want to compare the genotype concordance between two VCF files and I came across SnpSift, which seems to calculate the statistics that I want. However, the format of the results from my run differ from the format in the documentation. In this post, I will try to come up with the exact scenarios that...

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Converting PED into VCF

Updated 2015 August 25th: as suggested by Tim, I checked out PLINK 1.9 and found it much simpler to convert PED into VCF. I updated the post with instructions for performing the conversion using PLINK 1.9. Being late to the game of analysing genomic variants, I only recently discovered that IGV is capable of visualising...

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