BQSR using GATK BaseRecalibrator

Question

[Fatemeh Nabizadeh]

Hello everyone

I'm trying to use the BQSR tool for my patient's aligned bam file (using bwa + GRCh38.p14 reference primary assembly), but I get this error:

A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found.

reference contigs = [NC_000001.11, NT_187361.1, NT_187362.1, NT_187363.1, NT_187364.1, NT_187365.1, NT_187366.1, NT_187367.1, .............

features contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20................

I've downloaded the latest version of hg38 from https://www.ncbi.nlm.nih.gov/genome/guide/human/ while using the vcf files of databases (including dbsnp, Mills_and_1000G_gold_standard.indels, etc.) stored in https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0, which seems to be the issue:

The heading of my reference genome is like this:

NC_000001.11 Homo sapiens chromosome 1, GRCh38.p14 Primary Assembly

While the vcf files use chromosome numbers as :

chr1 2407130 rs2494427 T C

I don't know how to make the input files (reference and known-sites) compatible with GATK. Do you have any idea?

[barslmn]

Try downloading this genome.

Or this one.

[Fatemeh Nabizadeh]

Yep! The first one works! Thank U barslmn

My other question is that:

Some of the database files stored in the GATK resource bundle are not up-to-date (for example, the dbsnp's version is 138 while the 155th seems to be available now). How can this issue affect the training process in BQSR and VQSR? Is it more reliable to use the latest version of them?

[barslmn]

I never compared results of BQSR using different known sites files. GATK uses these files as a mask, so I am guessing it's better to use a newer dbSNP. You can use both and compare the results and make a decision based on that, or you can read more about their documentation how these files are used and make decision based on that. https://gatk.broadinstitute.org/hc/en-us/articles/360035890531-Base-Quality-Score-Recalibration-BQSR-

[Fatemeh Nabizadeh]

Thanks for your reply. I'll check that ;)