Question

BaseRecalibrator User error.

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19 days ago

ChumBucket2024 • 0

Hi everyone,

I am new to bioinformatics and I am struggling with GATK's somatic mutation variant calling pipeline.

I have completed most of the preprocessing steps: CreateSequenceDictionary, bwa index, bwa mem, and MarkDuplicatesSpark.

Yet, I've been struggling with a UserError on the BaseRecalibrator step.

For my known sites file, I have been using a C57/BL6 known sites vcf file I found on the Mouse Genome project website.

For the reference genome, I used the GRCm39 latest release.

My initial error with BaseRecalibrator was that my contigs were incompatible between reference and vcf file. I tried to solve this by using bcftools annotate --rename-chrs to alter the vcf files.

Yet, now I am getting a new error:

A USER ERROR has occurred: Input files reference and features have incompatible contigs: Found contigs with the same name but different lengths: contig reference = NC_000067.7 / 195154279 contig features = NC_000067.7 / 195471971.

At this point, I am not sure if I should just redo the analysis with an older version of the mouse reference genome, or if this error can be fixed. Any pointers?

GATK Mutect2 • 320 views

ADD COMMENT • link 18 days ago by ChumBucket2024 • 0

score 0 · Answer 1 · 2024-09-26

For my known sites file, I have been using a C57/BL6 known sites vcf file I found on the Mouse Genome project website.

Do you know what genome build this was based on?

For the reference genome, I used the GRCm39 latest release.

My initial error with BaseRecalibrator was that my contigs were incompatible between reference and vcf file. I tried to solve this by using bcftools annotate --rename-chrs to alter the vcf files.

Are you certain you are not mixing and matching genome builds. You can't do this. Results will be nonsense if you do.

Found contigs with the same name but different lengths:

This is more or less an indication that there is some sort of mismatch between the files you are using.