SomaticSignatures - Getting Started & Trouble Shooting
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jpluta26 • 0
@jpluta26-9948
Last seen 5.8 years ago

Hello, I am new to using bioconductor and new to genetics in general- sorry if this is an obvious question. I am trying to get started using the SomaticSignatures package. I have several TCGA subjects with .vcf files, and each subject has a .bam sequence file. I understand I need to load both the sequence and the reference to calculate signatures.

First, I converted the .bam file to .fa, and generated an index, using samtools. Then, I loaded the data as follows:

fa_A <- FaFile("sub1.fa")

dat <- readVcfAsVRanges("sub1.vcf", fa_A)

vr_A = mutationContext(dat, fa_A)

The last line returns: Error in value[[3L]](cone) : record 1 (1:12837280-12837282) failed

file: sub1.fa

as a starting point, can anyone tell me what this errors means?

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Are you sure you have the reference genome in your bam file?  Bam files normally contain sequencing reads and the position the align to in a reference, but not the reference sequence itself.

Given the TCGA samples are human, you can probably use the BSgenome.Hsapiens.UCSC.hg19 reference package, as in section 4.2 of the SomaticSignatures vignette.

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thanks for the reply, it was helpful. i was able to get some basic code working using the BSgenome reference package. the SomaticSignatures vignette states that a Fasta file can be used naturally, and i have this for each subject, so i was hoping to incorporate that. maybe i can figure out how to include the reference sequence in the fast file. thanks again for your help.