BQSR using GATK BaseRecalibrator
0
0
Entering edit mode
24 months ago

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?

GATK BQSR • 2.0k views
ADD COMMENT
1
Entering edit mode

Try downloading this genome.

enter image description here

Or this one.

enter image description here

ADD REPLY
0
Entering edit mode

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?

ADD REPLY
1
Entering edit mode

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-

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1179 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6